...why would you expect a civilian air terminal to have facilities large enough to accommodate a B-52?
Because civilian aircraft in general tend to be much bigger than military ones?
The same could be true of Trek starships, despite the fact that we tend to see really tiny freighters. A facility sized for the average starliner might well be able to accommodate six combat starships (say, Constitutions) or twelve Starfleet supply vessels (say, Sydneys) in the same volume.
Not that it'd be immediately obvious why a starliner terminal would need that protective shell any more than a combat starship base would...
Timo Saloniemi