The OP's point about damage still holds. After implanting the chronic arrays you have to wait about 3 weeks before recording (the area is silent). It is assumed that the responses are normal after that - and it seems so. But we have a lot of results from arrays that have no counterpart from single electrode recordings so we really don't know.

You are basically jamming a pincushion into the cortex. Trauma is inevitable. The denser the array the more the damage (the more mass you are jamming into cortex). You most likely have a perturbed cortex that has recovered from damage.

Is this the same as original intact cortex?