The physical system will do what it will do regardless of how we describing it. You knowing the microstate, will not affect how the system behaves.
You have discussed two different frameworks you can use to describe a system in thermal equilibrium.
The "classical mechanics" framework is that if you know the position and momentum of every particle (ie, the microstate), then you can evolve it using Newton's laws and know the state at every future time. From that, you can compute any observable you want (in principle). For example, if we put a pressure sensor in the gas, you could work out how each particle would interact with the sensor, and derive the precise reading as a function of time.
The "thermodynamics" framework is an effective description that we use when we coarse grain over irrelevant or unknown microscopic degrees of freedom. We start with the observables we actually can measure about the gas, such as the temperature, pressure, and volume, and think about what those look like in an equilibrium state and how they are related to each other. Using statistical mechanics, we can say that an ensemble of microstates subject to certain constraints will have a given average value for, say, pressure. Because the number of particles is so large, the fluctuations around this average are also small. In this framework, we assume that we don't know anything about the microstate, beyond the macroscopic observables. You could try to force your full knowledge of the microstate into this framework, and think of a distribution highly peaked around your microstate (with a zero or very small entropy), but you would be running against the spirit of this way of thinking.
Even though we give up information in the thermodynamics/statistical mechanics description, the two frameworks are consistent when they are both valid. If you measure the microstate (and didn't arrange for the gas to be in some super special state), then your microstate will simply be one draw from the distribution considered in statistical mechanics. Since we know what the average of observable quantities is in the distribution, and since the fluctuations around those averages are very small, then we expect the observables as predicted by your microstate will be the same as the statistical mechanics average quantities to a very good approximation.
Of course, there are questions for which you do need the microstate, and thermodynamics/statistical mechanics will not be sufficient. For example, you could ask for the the momentum of particle $j$ at time $t$. So knowing the microstate does strictly give you more information. However, usually these questions are not interesting and not even observable in practice. Another situation where you would benefit from knowing the microstate would be if you started the system in some bizarre, untypical state, like having all the particles of the gas in one corner of the container. This isn't strictly inconsistent with statistical mechanics, but of course you will get some results that are far from the average because you started in a state that was assumed to be very unlikely, so the statistical mechanics predictions will be inaccurate. However, the system will tend toward equilibrium, and sooner or later reach a more typical state closer to the average.