Edit after comments:
We have the experimental observation of fixed spectra coming from specific atoms. The same for nuclei, and both are stable in their ground state ( unless energetically disturbed or are unstable isotopes).
Quantum mechanical solutions reflect these experimental observations and the spectra of atoms and nuclei have been fitted with potential models, shell models.
when we talk about the elementary problems in quantum mechanics like particle in a box, we first calculate the energy eigenfunction.
This is a very specific problem and has set of eigenfunction. The particle can only be in one of these eigenfunctions , not in a superposition. The potential is very specific and the energy operator, the Hamiltonian, is known . If the electron, for example , were in a superposition of energy states about the hydrogen atom, it would have a probability to be in a higher than ground state without external energy input, and a probability then to decay to the ground state, violating energy conservation.
Then we say that the most general state is the linear combination or superposition of these basis eigenfunctions.
This is a general statement when the potentials are not specified, i.e., the Hamiltonian , is not specified. Then one has the possibility in order to describe the state of a particle to use the set of eigenfunctions coming from other specific quantum mechanical operators, for example solving for the eigenfunctions of the momentum operator .
Example:
Consider a free electron in one dimension that is described by the function
$$\Psi(x)= C_1\psi_1(x) +C_2\psi_2(x)$$
$$\psi _1(x) = \left ( \frac {1}{2L} \right )^{1/2} e^{ik_1x}$$
$$\psi _2(x) = \left ( \frac {1}{2L} \right )^{1/2} e^{ik_2x} \tag {5-23}$$
where k1 and k2 have different magnitudes. Although such a function is not an eigenfunction of the momentum operator or the Hamiltonian operator, we can calculate the average momentum and average energy of an electron in this state from the expectation value integral. (Note: in-this-state means described-by-this-function.)
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The function shown above belongs to a class of functions known as superposition functions, which are linear combinations of eigenfunctions. A linear combination of functions is a sum of functions, each multiplied by a weighting coefficient, which is a constant. The adjective linear is used because the coefficients are constants. The constants, e.g. $C_1$ and $C_2$ in the , give the weight of each component ($\psi_1$ and $\psi_2$) in the total wavefunction.
In the above example the $\psi_1(x)$ the $\psi_2(x)$ are an eigenfunction of the momentum operator and also the Hamiltonian operator ( since no potential in the problem) although the linear combination function $\Psi$ is not.
In general when the Hamiltonian is known the bound states are defined and the particles will fill up the energy levels starting from the lowest state sequentially. To get to a point where a superposition of eigenfunctions is necessary the system will not be a simple potential problem of a stable atom. A linear combination of energy eigenfunctions will be needed for the description of an ensemble of particles where some are in excited states and there are energy inputs by radiation, for example.
For your example after the edit: if the simple potential model is adequate in describing the system one avoids the complexity of linear combinations: the key is " nearly free", so there exists a solvable potential and that is used.