The point is that despite owning 4 Z-95s once I've gotten Most Wanted I still will be unable to run 4 of them despite having the other pieces I need because for some strange reason the dials will not be compatible.
I don't think it's strange at all.
The baseline is very simple: One purchased ship = one flyable ship, and that is restricted by faction.
If you buy one Z-95, you have enough cards and baseplates to run two, but only one dial and ship. This is obviously intentional. One ship purchased means one ship on the board, spare components aside.
Most Wanted is creating a scenario which fills part of that component gap by giving you extra spare components via crossover - in this case the ship model itself. So you feel like they should let you cross over the remaining component.
But that's not the way they intend it to work. I honestly don't see this as any different than asking why they don't give us a second dial with each ship (to go with the extra baseplate) and make the models optional. That would give you multiple ships out of the same box just the same.
The obvious intent is that each ship you buy provides some limiting component so that you can only achieve one playable ship. You can dislike that, especially as the component gap closes, but there's certainly nothing strange or dumb about it.