Not quite- the military presence in TTFAW is incidental. They were an USAF resupply crew delivering to a civilian scientific survey & research base and just happened to be there for all the fun. The military in Aliens was on an active bughunt.
As for the characters in JCTT, it's not so clear. AFAICT, the only person addressed by any kind of title is the Doctor- everyone else goes by their last name. IOW, we have no idea as to wethernthey are military or not. (As I recall, the same is true of the story, but don't quote me.)
