It's canon that bounty hunters have worked for both the Empire and Rebels at times. Whoever had the best deal at the time. So, what about a "Hired Bounty Hunter" upgrade card that would allow you to use a Scum ship in a Rebel or Empire squad? Maybe a 5 point card with no slot requirement, just the points?

That would be interesting, but it would probably be a crew with a defect in it like, "Your scum ship cannot exceed 40 point (upgrades and pilot combined)."

Honestly I would like to see Imperial conversions of Scum Bounty hunters in the same way that Boba Fet was converted over into scum. So Imperial IG-88s and Imperial Dengar (maybe with the rumored upgrade bar) and Imperial YV-666 would be the thing to see.

As for mixing well that is probably better in an alternative format. I have one right here, and yes it is FAQ compliant. Y2K-wing won't effect it.