Heh, I love starcraft. Many fond memories from my undergrad days, playing with my roommates. I won't be getting SC2 anytime soon, though--my computer couldn't handle it. Curse the profusion of 3d games and my lack of a graphics card! Maybe many people on this forum dislike starcraft because it's almost the inverse of dwarf fortress. DF is a small, indie game with a focus on broad, realistic simulation. It's still a bit rough around the edges but we all love it. Starcraft is a big budget popular game with a focus on narrow, abstracted combat with an emphasis on polished gameplay. For all those who say they hate RTS's though, I ask you...what do you think DF is? It's played in real time, it requires strategy! Sure, you can pause it, but you can pause any RTS if you are playing single player. Sure, it has a stronger emphasis on "city building" than the average RTS, but in my estimation it still falls into the category.
Mmm, also, I don't think you can blame blizzard for reducing creativity in game development, since I can think of at least two genres of games that were spawned from the map editors for starcraft and warcraft....tower defense (which has gone on to inspire a profusion of flash games) and Defense of the Ancients (which has inspired at least one mass market game).
As for the OP, I think it really is a reference. First of all, the "Bay 12". For this to be random, consider the choices that must have lead to it's presence. First, the devs could have not placed a room number at all. Since you don't actually walk the corridors to find the place, this could have easily happened. Second, they had to choose "bay" as the descriptor of the room--when they could have easily chosen "sector", "level", "room", or some other term. Then they had to provide it with a number, which clearly could have been any number between 1 and 12, and probably anything between 1 and 99. So it's highly unlikely for them to randomly pick "Bay 12" as opposed to leaving it blank or using another number or term--maybe 1/800 if all options were equally likley (an unreasonable assumption, mind. but still). So "Bay 12" is likely a reference to either DF or aliens. Now, both have been referenced in Blizzard games before: DF very clearly in WoW, likewise Aliens in the original Starcraft (the dropship says "in the pipe, 5 by 5"). So both are possibilities. To determine which is being referenced we should consider the context. On the pro aliens side, we have the general context (a bay in a spaceship) and the fact that starcraft contains some xenomorph knockoffs. On the pro DF side we note that the room holds a short, stocky technologically proficient miner with notable facial hair from the planet Moria. I have to side with DF here, because that reference is more specific. If the room contained an Zerg queen instead of a dwarf stand-in, I'd go the other way. However, it's worth noting the possibility that the reference is to Bay 12 in particular since it can reference BOTH df and aliens.
Not that it really matters at all, but analysis is fun!