I have been struggling with rules to build armies in Skirmishes. The rules to the core game clearly state that you can build >either< a Rebel, Imperial, or Mercenary army. Imperial upgrade cards (Temporary alliance) then give you the option to include up to 2 Rebel or Mercenary cards as Imperial player. No such thing exists for the Rebels, >implying Rebel armies have Rebel deployment cards only<.

Now, in Jabba's Realm expansion (and maybe others?), all "Rebel" heroes (Onar, Vinto, and Shyla) are of the Mercenary faction. According to core game rules, the Rebel army cannot include these deployment cards, but the Imperium could, which doesn't make any sense thematically. No modification to this core rule is included in the Jabba's Realm rules.

Is there a new rule I am missing that now (with expansions) allows the Rebel player to have (an unlimited number?) of Mercenary deployment cards in their Skirmish army?

If you could point me to an official rule for this that would be great; I have been looking in all rulebooks I have, as well as in the BGG and FFG forum, but couldn't find an answer to this very basic question.

Thank you,
Roland

Nope, nothing has changed. The only way to include Merc deployments in Rebel lists is with Saska Teft. Vinto, Onar, and Shyla are all of the Merc faction, so you cannot put them in Rebel lists without Saska.

Mercs can include up two Rebel deployments via their own version of Temp Alliance. They can also include droids of any faction using Elite Jawas. And then of course Empire can include up to two Merc deployments using their Temp Alliance as well.

Those are the only ways bring units across factions IIRC.