I'd wager what happened is that even though the script and original book call for a courtroom the war museum was chosen instead because it was both convenient to film in and quite visually striking (the room his cell is in particularly) and all dialogue that references what the building actually is were taken out. It's weird that they just left the war museum sign in either way, though.

Mmm... what's always been interesting about Alien to me is the Xenomorph as this terrifying, unknowable and practically unstoppable force, when you outfit your protagonists with mech suits to fight them and then have people getting high off the alien's bodily fluids you kind of kill that.

There's a lot more going on in "Ridley's shitty prequels" than just crews being killed by an Alien one by one. Making a movie where Xenomorphs are let loose in a Wal-Mart just sounds like Alien Vs. Predator 2.