As for the part of your post about Bosses in the Flying Fortresses not being there or regular mosters that seems to not show graphically, i myself have not encountered such bugs so id pretty much guess it doesnt have to do with how the game was made, maybe more to do with a conflict between the game and your own computer.
There probably is some conflict but just to get one thing strait im sort of a PC freak so my rig is sort of off the chart regarding components. (never really believed in BS like crossfire or SLI so thats the only thing i dont have and saves me alot of problem regarding game glitches)
And guessing by the fact that it only happen in those zones (and not only to me if you google it) and everything else is working perfectly i actually suspect exactly the opposite of what your stating. If it would be my PC as cause then it wouldn't be so isolated to specific area's of the game.
