When one studies quantum mechanics under a more rigorous point of view, the very first postulate states that the underlying Hilbert space $\mathscr{H}$ is separable. This means that $\mathscr{H} $ has a countable orthonormal basis.
I remember when I took a first course in quantum mechanics the first part of the course was dedicated to solving the Schrödinger equation $H\psi = E\psi$ to find the eigenvalues of the Hamiltonian. When the system was bounded, the Hamiltonian had only a countable set of eigenvalues $\{E_{n}\}_{n\in \mathbb{N}}$ and its corresponding eigenvectors defined a basis for the Hilbert space. This was done, e.g. to study a particle in a square well, the harmonic oscillator or even the Hydrogen atom.
At a first sight, I thought the separability condition was reasonable because one was trying to find a basis of eigenvectors of the time-independent Hamiltonian $H$. This was for me the basic machinery of quantum mechanics, as the aforementioned examples would suggest.
However, when I started studying the mathematics of quantum mechanics more deeply, one finds out that the Hamiltonian is supposed to be a self-adjoint operator on some densely-defined domain on $\mathscr{H}$ and, of course, it is not always the case it has a countable set of eigenvectors.
It is clear to me that the separability condition is necessary. What is not clear is what it means when it is not connected with states of well-defined energy. For instance, suppose we have a many-particle quantum system described by a Fock space $\mathcal{F}(\mathscr{H})$. To study bosonic or fermionic Fock spaces one usually uses a countable basis for $\mathscr{H}$ to find a countable basis for $\mathcal{F}(\mathscr{H})$. If $\mathscr{H}$ has a countable basis of eigenvectors of the Hamiltonian of a single particle state, each associated to an energy $E_{n}$, it is clear that a state $|n_{1},n_{2},...\rangle$ of the Fock space can be thought as a state with $n_{1}$ particles with energy $E_{1}$, $n_{2}$ particles of energy $E_{2}$ and so on. If, on the other hand, $\mathscr{H}$ has a countable basis which has nothing to do with the Hamiltonian, then the states $|n_{1},n_{2},...\rangle$ mean nothing to me because I don't know what this basis represents.
So, what is the point of having a basis for $\mathscr{H}$ which has nothing to do with the Hamiltonian? Is it physically relevant? If so, what it represents?