The shells are not actually shells. In modern theory, as opposed to the flawed Bohr model, electron position is described by wavefunction probability densities. These are continuous functions and they overlap with each other. In principle if the wavefunction overlap is equal to zero exactly, then there is no allowed transition for the reason you mention. In most cases, overlap is nonzero (although it can be quite small), so transitions are allowed.
I am not sure if I get you right, but I think what you say is not correct.
1) Eigenfunctions to different Eigenvalues of the Hamiltonian (=Energy levels) are always orthogonal to each other (no overlap). (not considering degeneracies for now).
2) a transition is (in first approximation) allowed, if the transition dipole moment is non-zero, which doesn't have much to do with overlap.
to the original question:
1) quantum theory does not describe trajectories of individual electrons. It uses wavefunctions, which have some relation to probability densities. But then again, you can't distinguish electrons, which means you can't say that electron1 has done a transition, only the whole system can do a transition. (you could argue with the hydrogen atom, though)
2) Here it comes hard for me, since I am not an expert at all: As far as I know, the modern theory uses the formalism of "second quantization", which uses annihilation and creation operators. Regarding the formalism, a transition is described as an electron being annihilated from one state and created in another. But I can't argue how much this actually describes the picture physicists have to day or it's just pure formalism.