First off, we know that there will be different factions. We also know that there are several ships that have pilots for different factions. Also, this is from the standpoint of a new player and limiting duplicate skus

Limiting skus is important to most stores to minimize order quantity on the shelves. Space is a finite quantity and many don't have room to show every product effectively, which results in lost sales.

Now the y-wing makes sense to repackage, as many players will want multiples anyway. With many of the astromechs working for both, there would be value likely, but goes against the above.

But ships like the HWK-290 make a lot of sense to have a multi-faction release. The title works for both, and a release that has both rebel and scum pilots may lead a player to try/start collecting another faction. The factions could be noted clearly on the packaging.

Other options are the Original and Sequel Millenium Falcon - especially with the possibility of the Pristine Lando Cape Conveyor.