Since release it has used the modifiers of the host empire. One little wrinkle is that way back when, if I'm remembering correctly, there were far more global resource modifiers that *would actually apply*. Now that most resource modifiers apply to jobs, they don't apply to branch buildings, and so even if you build your Private Mining Consortium on the most Dwarven of Subterranean mining specialists, you'd be lucky to see +10% to the mineral production. Unity happens to be the one resource that most empires have a few global modifiers for.
It really is a shame, as making more modifiers apply to branches would make where to build them and what to build on them an interesting choice, rather than always the same.
If you ask me, Branch Buildings should do something similar to the new Overlord Holdings. Provide a job that the host can choose to work, which gets all appropriate bonuses, and give the Megacorp a cut. This makes Megacorps more useful in actually providing jobs, allows bonuses to apply properly, and is satisfying thematically.