I already gave a very obvious example of how the measurement apparatus and the system may start in energy eigenstates and end up each in superposition.
AND IT MUST, BY DEFINITION of what a measurement apparatus must be able to do. It must start with some initial state, and end up in measurement result states. This can _only_ happen if there is some way to get to all those different states. The measurement process cannot be diagonal in Hamiltonian eigenbasis