My guess is that this has to do with information of the observer. In other words, the canonical ensemble refers to the situation where the system $A$ has been placed into the reservoir $R$, and no further information is known. In that case, as that observer, you couldn't say that $A$ was at $E_{\text{cold}}$ at time $t_0;$ you could only ever give a (time independent) probability distribution for the energies of $A$.
Jaynes' Maximum entropy approach to deriving (macro)canonical distribution is a valid point of view, but the "traditional" reasoning in statistical physics is somewhat different. (See, e.g., Microcanonical ensemble through Maximum Entropy method.)
Thermodynamic equilibrium
In this traditional approach the equilibrium is usually defined by formulation like "all the fast relaxation processes have ended, and all the slow relaxation processes are too slow on the relevant time scale". In other words, for practical purposes thermodynamic equilibrium is approximate. E.g., very slow molecules may never hit the walls of the container during the observation time, but this doe snot prevent us from extending integral to zero when calculating pressure - the error is negligible.
Thinking of the size of the error leads us to draw a distinction between situations (1) and (2) mentioned in the Q.: by fluctuations in statistical physics we usually mean deviations of the order of $1/\sqrt{N}$ - i.e., the error in our approximation of the distribution by equilibrium one, which vanishes in thermodynamic limit. These fluctuations can be very large, but such large fluctuations are very rare/improbable - e.g., the probability that the Red Sea opened in front of Moses is finite, but so small, that we can neglect it for all the practical purposes, and confidently say that it has never happened. (Remember, that the relevant scale here is $e^{N_A}$, where $N_A\approx 10^{24}$.)
There are also situations that one often describes as equilibrium, but which are really stationary states, because they are characterized by permanent energy/matter fluxes. E.g., the surface of the Sun can be considered to be in equilibrium, characterized by temperature, usual statistical distributions, etc. In fact, this surface constantly loses energy via radiation, and this energy is resupplied by the thermonuclear reactions within the Sun, but for many practical purposes it is irrelevant. (See How does radiation become black-body radiation?.)
In the context of deriving hydrodynamic equations from Boltzmann equation, one also speaks o local equilibrium - a Boltzmann-like distribution with parameters (temperature and potentials) slowly varying through space, which however turns to zero the collision integral.
Ergodicity
Another factor to consider is the assumption of ergodicity, which underpins the "traditional" derivations. It means that in practice we average the state of the system over a rather long period of time, rather than over an ensemble, assuming that the two averages are equal. This directly addresses situation (1) in the Q.: fluctuations take place all the time, but they average out during the observation time.
On the other hand, a system genuinely driven out of equilibrium (situation 2) would show evolution, even with the averaging. In essence, we deal with quantities defined as:
$$
U(t)=\frac{1}{T}\int_{t-T/2}^{t+T/2}u(t)
$$
In equilibrium $u(t)$ - the instantaneous value - is changing all the time, but $U(t)$ remains nearly constant (to required precision).
See also: What maximizes entropy?
Remark
A probability of a single microstate under Boltzmann distribution is $p_i\propto e^{-\beta E_i}$. The probability of any microstate of energy $E$ is $p(E)\propto\sum_i\delta (E-E_i)e^{- \beta E_i}=\rho(E)e^{- \beta E_i}$ (I admit that the proportionality sign makes this distinction mathematically irrelevant, but it comes back into force when calculating the partition function or discussing the DOS.)
Appendix
In response to the comments, I have reviewed about a dozen introductory texts on statistical mechanics, in search for a clear definition of statistical equilibrium. I stress here that I am talking about statistical mechanics and not thermodynamics texts. I gave found that some of them forgo defining equilibrium completely, assuming perhaps that it is self-evident. Of the rest, I found no a single satisfactory definition, although the main outlines are clear - I add the quotes below.
In general, there are several types of definitions:
Empirical
You know it is an equilibrium when you see it. These definitions rely on our everyday experience that systems evolve towards an equilibrium state. This is a middle ground between the intuitive understanding and the thermodynamic definition below.
Thermodynamic definition
Equilibrium is a state stable against spontaneous changes. This is readily tied to entropy, and sometimes recast as a state in which entropy has its maximum (or more generally, specific thermodynamic potentials have extremum.) I think this definition belongs to thermodynamics rather than statistical physics, since it deals purely with macroscopic quantities and grounded in phenomenological observation.
Traditional definition
Finally, there is what I called above traditional definition, which comprises the following characteristics (although no single book below cites all of them):
- The system experience no macroscopic changes (processes), although it still evolves microscopically (fluctuations)
- The system reaches this state after an infinitely long wait (a more refined version of this statement is that the time is sufficiently long for "fast" relaxation processes to run out, but not too long for the "slow" processes to manifest themselves. This allows to incorporate, e.g., applying stat physics to elementary particles with long but finite lifetime or neglect slow chemical reactions - I heard this many times, but I couldn't find the exact reference.)
- There are no macroscopic fluxes of energy or matter
Quotes
Landau&Livshitz "Statistical physics, Part 1"
If a closed macroscopic system is in a state such that in any macroscopic
subsystem the "macroscopic" physical quantities are to a high degree of
accuracy equal to their mean values, the system is said to be in a state of
statistical equilibrium (or thermodynamic or thermal equilibrium). It is seen
from the foregoing that, if a closed macroscopic system is observed for a sufficiently long period of time, it will be in a state of statistical equilibrium
for much the greater part of this period. If, at any initial instant, a closed
macroscopic system was not in a state of statistical equilibrium (if, for example, it was artificially disturbed from such a state by means of an external
interaction and then left to itself, becoming again a closed system), it will
necessarily enter an equilibrium state. The time within which it will reach
statistical equilibrium is called the relaxation time. In using the term "sufficiently long" intervals of time, we have meant essentially times long compared
with the relaxation time.
Reif "Statistical Physics"
A system of many particles (such as our gas)
whose macroscopic state does not tend to change in time is said to be
in equilibrium.
Tanaka "Methods of Statistical Physics"
The thermodynamic process is a process in which some of the macroscopic
properties of the system change in the course of time, such as the flow of matter or
heat and/or the change in the volume of the system. It is stated that the system is in
thermal equilibrium if there is no thermodynamic process going on in the system,
even though there would always be microscopic molecular motions taking place.
The system in thermal equilibrium must be uniform in density, temperature, and
other macroscopic properties.
Smirnov "Principles of statistical physics"
In the course of the evolution of the system
an individual particle can change its state, but the average number of particles in each state
is conserved with some accuracy. Such behavior in a closed system is called thermodynamic
equilibrium.
Sadovskii "Statistical physics"
When a macroscopic system is in (thermodynamic) equilibrium, its macroscopic
characteristics (temperature, volume, pressure etc.) remain constant in time, though
its microscopic state continuously changes and we do not know it at all (i.e. where
precisely is its phase point on the ergodic surface at the given moment in time)
Reichl "A modern course in statistical physics"
Since the equilibrium state is, by definition, a state which is stable against spontaneous changes, Eq. (2.49) tells us that the equilibrium state is the state of maximum entropy.
Fitzpatrick "Thermodynamics and Statistical Mechanics"
Let us consider an isolated system in equilibrium. In this situation, we would expect the prob-
ability of the system being found in one of its accessible states to be independent of time. This
implies that the statistical ensemble does not evolve with time. Individual systems in the ensemble
will constantly change state, but the average number of systems in any given state should remain
constant. Thus, all macroscopic parameters describing the system, such as the energy and the volume, should also remain constant. There is nothing in the laws of mechanics that would lead us to
suppose that the system will be found more often in one of its accessible states than in another. We
assume, therefore, that the system is equally likely to be found in any of its accessible states. This is
called the assumption of equal a priori probabilities, and lies at the heart of statistical mechanics.
In fact, we use assumptions like this all of the time without really thinking about them.
It follows that if a stable equilibrium state has been attained [i.e., one in which no further spontaneous processes (other than random fluctuations) can take place] then this state is such that S
is maximized. In other words, it is the most probable state of the system, subject to the given
constraints.
Chandler "Introduction to modern statistical mechanics"
Experimentally we know that isolated systems tend to evolve
spontaneously toward simple terminal states. These states are called
equilibrium states. By simple we mean that macroscopically they
can be characterized by a small number of variables.
Virtually no system of physical interest is rigorously in equi-
librium. However, many are in a metastable equilibrium that usually
can be treated with equilibrium thermodynamics. Generally, if in the
course of observing the system, it appears that the system is
independent of time, independent of history, and there are no flows
of energy or matter, then the system can be treated as one which is at
equilibrium, and the properties of the system can be characterized by
E V, «!,..., nr alone. Ultimately, however, one is never sure that
the equilibrium characterization is truly correct, and one relies on the
internal consistency of equilibrium thermodynamics as a guide to the
correctness of this description. An internal inconsistency is the
signature of nan-equilibrium behavior or the need for additional
macroscopic variables and not a failure of thermodynamics.
Huang "Statistical mechanics"
Thermodynamic equilibrium prevails when the thermodynamic state of the system does not change in time.
Mandl "Statistical Physics"
More generally, let us consider an isolated system. This system may be in a state containing all sorts of pressure differences, temperature gradients, ihomogeneities of density, concentrations, etc. A system in such a state is of course not in equilibrium. It will change with time as such processes as pressure equalization, thermal conduction, diffusion, etc., occur. Left to itself, the system eventually reaches a state in which all these pressure gradients, etc., have disappeared and the system undergoes no further macroscopically observable changes. We call such a state an equilibrium state.
Wikipedia Thermodynamic equilibrium
Thermodynamic equilibrium is an axiomatic concept of thermodynamics. It is an internal state of a single thermodynamic system, or a relation between several thermodynamic systems connected by more or less permeable or impermeable walls. In thermodynamic equilibrium, there are no net macroscopic flows of matter nor of energy within a system or between systems. In a system that is in its own state of internal thermodynamic equilibrium, not only is there an absence of macroscopic change, but there is an “absence of any tendency toward change on a macroscopic scale.”1
A collection of matter may be entirely isolated from its surroundings. If it has been left undisturbed for an indefinitely long time, classical thermodynamics postulates that it is in a state in which no changes occur within it, and there are no flows within it. This is a thermodynamic state of internal equilibrium.[5][6] (This postulate is sometimes, but not often, called the "minus first" law of thermodynamics.[7] One textbook[8] calls it the "zeroth law", remarking that the authors think this more befitting that title than its more customary definition, which apparently was suggested by Fowler.)