The way I think of things like 2fort or Granary is Valved flipped through stock photos looking for an average scene that looked interesting.. in 2fort's case, it's part of some kind of canal system, and Granary is straight out of the US midwest. I mean, this is basically granary right here:
https://www.google.com/maps/place/D...2!3m1!1s0x52ae527e782e37ff:0x90fdbf76eb580c72
Then they pervert the interior spaces with the TF2 shtick. No one questions this setup because hey, it's a secret spy base. Of course they'd stash missiles in an industrial site!
That's not the only way to do it though, gameplay trumps everything. Upward makes absolutely no sense when you step back and study it, and yet it'd be a contender to head the list for Valve's best map. The buildings clearly take design hints from early/mid 1900's mining installations, but those facilities are always built into the side of a mountain, not on top of it.
Example:
https://www.google.com/search?q=ind...a=X&ei=bywkVKuCHZWiyATBlIK4Bg&ved=0CAgQ_AUoAw
That's basically Upward right there. Well, it was before all the buildings collapsed and the metal rusted away.
At any rate, I guess the takeaway is not that the factions in TF2 are "incompetent" but rather the game world is a child's idea of making normal mundane things awesome. What if that mountain had a doomsday device in it? What if you could fight in a lumber yard with spinning sawblades everywhere? Of course that would be awesome.
That makes the mapper's job a task of merging adult sensibility and childlike imagination in a way that makes sense, but not too much sense.