As far as I know, to capture a V-Base, take out the acks and drop the little green men then pray that LTAR doesn't come pouring out of the VH if you didn't destroy it.
You are correct that there seems to be a building that won't come down. I have done everything short of dropping a nuke on it. It won't come down at airfields either. However you never did have to drop VHs or other buildings to capture a V-Base. Towns have been the only facilities that needed to have all the buildings destroyed.
Hope this helps.
LTARsqrl
