This is more of a question for the future, but since subfaction ships can be included in a list of the over all faction, say Resistance ships in a Rebel list, can Rebel only upgrades be put on Resistance ships and vice versa?

I apologize if this has been asked and answered already. I searched, but I couldn't find an answer.

Yes, they can. The sidebar on the factions says:

There are three primary factions in X-Wing: Rebel, Imperial, and Scum. The Rebel primary faction consists of the Resistance and the Rebel Alliance. The Imperial primary faction consists of the First Order and the Galactic Empire. The Scum primary faction consists of the Scum and Villainy subfaction.

So the "Imperial/Rebel only" restrictions refer to the primary factions, and are available to ships from either subfaction of that primary faction. If a future upgrade were printed with a "Rebel Alliance only" restriction, then that would not be legal to equip on a Resistance ship.

This is more of a question for the future, but since subfaction ships can be included in a list of the over all faction, say Resistance ships in a Rebel list, can Rebel only upgrades be put on Resistance ships and vice versa?

I apologize if this has been asked and answered already. I searched, but I couldn't find an answer.

If they weren't there would be no ships that can use them at all. The ships that used to be Rebel ships are now Rebel Alliance and the ships that were Imperial are now Galactic Empire.