I am trying to understand what you mean by the following two statements.
Let's consider the four states in the excited Hydrogen atom (no spin), ##R_{20}Y_{00}##, ##R_{21}Y_{11}##, ##R_{21}Y_{10}##, ##R_{21}Y_{1\bar 1}##. Let's call this set of basis states "Basis 1". The unperturbed Hamiltonian using t"Basis 1" will be diagonal with ##E_2## along the diagonal. If you measured the energy of this hydrogen atom, you will get ##E_2##. If someone asked you "what state is this hydrogen atom after the measurement?", the answer is "I don't know."
Now suppose you choose 4 orthonormal linear combinations of the four states and call your choice "Basis 2". Calculating the energies and constructing the Hamiltonian is trivial. Measuring the energy still gives ##E_2## as a result and as for the state of the atom after the measurement, the answer is still "I don't know". I'm sure you agree with all of this so far.
Now here comes the perturbation. We put a uniform magnetic field in some direction relative to our lab and go about our business of measuring energy or orbital angular momentum or both. This is where Griffiths's "good states" come in. Basis 1 are the good states if (and this is an important if) we identify the direction of the magnetic field as the axis of quantization of the spherical harmonics. Then the Hamiltonian is already diagonal and we have nothing more to do. The energies are ##E_2## for ##R_{20}Y_{00}##, ##E_2+\epsilon## for ##R_{21}Y_{11}##, ##E_2## for ##R_{21}Y_{10}## and ##E_2-\epsilon## for ##R_{21}Y_{1\bar 1}##. If you measured the energy, you would get ##E_2##, ##E_2+\epsilon## and ##E_2-\epsilon##. If you get ##E_2##, you would still not know what state the hydrogen atom is in after the measurement, but that would no longer be the case for the non-degenerate states. If the measurement returns ##E_2+\epsilon##, then you know that the atom is in state ##R_{21}Y_{11}##.
If, however, we chose "Basis 2" and chose the magnetic field in the x-direction relative to the quantization axis, we will end up with a Hamiltonian with a whole lot of off diagonal elements that we will have to diagonalize. Say that we do that and then proceed to get the eigenvectors. We will end up with linear combinations of the "Basis 2" states which. lo and behold, are nothing but ##R_{20}Y_{00}##, ##R_{21}Y_{11}##, ##R_{21}Y_{10}## and ##R_{21}Y_{1\bar 1}##.
When we are done and turn the magnetic field off, we are back to where we started. So can you explain to me what you mean when you say that all the states are not equally likely when the perturbation is gone? In what sense are they not equally likely?