I have already read the following discussions and would like to point out that my question goes in a different direction:
If superposition is possible in QM, why do we often assume systems are already in their eigenstates?
Why is it often assumed that particles are found in energy eigenstates?
According to my current understanding, the labels that we assign to electrons in a multi-electron atom follow a hierarchy. The hierarchy is based on how precise and informative we want to make the description of the electrons. The simplest one is the electronic configuration, wherein we 'fill' the known eigenstates of a Hydrogen-like system with electrons, using a given set of rules (Pauli's exclusion principle, Hund's rule etc.) without considering any interactions among them. The next label in the hierarchy is a 'term', which is defined by considering spin-spin as well as orbit-orbit coupling resulting in the total spin and angular momentum quantum numbers $\textit{S}$ and $\textit{L}$ the system. This is followed by a 'level', which additionally specifies the quantum number $\textit{J}$, and finally the 'state', which specifies an $\textit{m}_J$ along with the first three.
My question is about the step in which we write electronic configurations. We start by making an energy level diagram of known eigenstates of hydrogen-like atoms and start to fill them up. We denote electrons as half-arrows whose direction represents their $m_s$ state. My first question lies here. The definition of $m_s$ relies on a well defined $z$-axis and hence a coordinate system. I understand that we can always choose the coordinate frame so as to have the first electron in an $m_s$ eigenstate. However, why do we assume that all the subsequent electrons would also be in $m_s$ eigenstates in the same coordinate frame?
My second question is about the act of 'placing' a half-arrow into one of the sketched out $m_l$ states, implying that they always have simultaneous eigenstates. Is there something fundamental that's preventing the electron from being in the superposition of $m_l$ states while being in an $m_s$ state and vice versa?
My first guess was that the spin of the first electron influences that of the others' to align with it. Similarly, that the electron 'prefers' to be in simultaneous $m_l$ and $m_s$ states because of energy considerations like the one discussed in L-S coupling. However, according to my current understanding, we only start incorporating those forms of interactions $\textit{after}$ having written the electronic configuration first, which is more of a symbolic (not representative of a physical reality) first step to get to the actual physical state (one specified by $\textit{L}$, $\textit{S}$, $\textit{J}$, $\textit{m}_J$). Is it that the electronic configuration is also a physical description and that coupling interactions are guiding it from the very beginning? Or is it also one of those cases where superposition is a genuine possibility that we neglect to consider the simplest case?