I've never played in a Rogue Trader campaign, but it seems to me that they have a similar problem: despite everyone starting at Rank 1, one of the PCs is the 'Royal Captain-Lord' and all of the other PCs are merely his lackeys. How do they handle the radically different levels of authority in that game?
I think RT gets around it by saying that many of the other classes are either people hand-[icked by the RT (they SHOULD get along) or specialists that the RT can't live without, or emulate. Yeah, he's in charge, but like a pirate ship, he's only in charge while the crew tolerates it. If the Navigator says "I'm not steering", the RT, and everyone, can be screwed. Do you shoot the navigator? Good luck sailing, and the other Navs will not look smiling on the summary execution of one of their senior family members. Lock him up? He can't steer from there. Explorators are the same; your average RT could no more easily configure the plasma drive than steer through the Warp. He needs to keep the AdMech aboard happy, so that the ship stays viable. The Seneshal probably knows his secrets, and on down the list. It doesn't always work, but the RT is less well served aceing a fellow player than a Commissar punishing weakness. Of course, mileage varies, as always.