I know that some of the missions stretch the boundaries of the whole "Battle of Endor". In fact, as it stands, I'm pretty sure that mission still has a random crash that even Goober couldn't figure out the cause of. That was a while ago, so it's quite possible it's easier to locate and fix now, though we aren't on the final pass yet. It's something that still has to be fixed. There are a few missions like that. About the effects and the HTL ships, those are more questions for the modders.
Yeah, it's a Special Operations Command wing, and yes, it's a mixed wing. Yes, Vasudans are a big part of the storyline, considering there are no Shivans in BWO.
I haven't played all the missions recently, but I do seem to remember the Mentu being there a few times, not all that refreshed on the Aeolus' we use.
I should really go back and play all these again.