I don’t remember if it was in the trailer, but Sabotage was definitely in the 2009 Star Trek, and a “Body Movin’” remix is in Into Darkness. I kinda want to say they used a Two Steps From Hell track on the trailer.
Yeah, I don’t get it, either.
As far as the parody goes…I don’t know. I know I’ve seen the argument that Yauch said in his will “no advertisements” (which means they can’t just work it out amicably, I guess) and they seem like massive freakin’ hypocrites defending a License to Ill song on the grounds of copyright violation. On the other hand, it’s clearly supposed to just be turning the Beastie Boys song on its ear. Then again, it’s a parody of satire (honestly, the album is pretty much satire), and that particular track is (imho) an original work.
My gut wants for the Beastie Boys to lose this one, but my gut isn’t a lawyer.