Most passholders would therefore have multiple resort stays under a single AP. The question is whether the database architecture would allow linking multiple reservations to a single AP.
In all other situations, FP+ rights could be managed by some ticket identifier. Buy a 7-day MYW, get 7 days worth of FP+ rights. Buy an AP, get 20 per quarter (or whatever).
In your example, you're talking about co-mingling FP+ rights which are issued on the basis of type of ticket along with rights linked to a hotel reservation.
Those aren't insurmountable obstacles but the system would have to be carefully designed to allow it to happen. They would have to make sure that the resort entitlements don't eat into the AP entitlements, and vice versa. It's very much an area where programming glitches or customer misunderstandings could cause ongoing problems.
It would be more straightforward (IMO) if Disney intended to give all resort guests some additional FP+ perk on top of whatever their ticket allows. For instance, imagine that resort guests get two FP+ per day on top of the ones allowed by their MYW tickets or APs. That way you're keeping the resort entitlements and park ticket entitlements entirely separate, albeit linked under a single MagicBand / KTTW card.