PVE LMAO, is there such a thing in this game? For most pve encounters are just the time in between wiping out bluesuits, taking towns, and heading to NCR to grief. For others pve encounters are the time when you sit begging to run to the exit grid before some uber pvp build drops in and takes you out in one turn. You might stop to fight if you actually got to level up some, but smart moneys on running. There is some risk in facing the pve portion of the game but it is sooooo far out shadowed by the risk of everything the pvp brings on you.
The military base was where the FEV was, and conversely it's not unreasonable to say that some troops went to where their boss was to see what was up. So encountering mutants everywhere, not so bad, but the severity of them in the boneyard, especially against the stuff that they fight, the boneyard in all technicality should be overrun with mutants, bye bye fortress lol.
I really wish I had some idea to help out. All I know is how I play, and I go for quests, pve, and exploration. And most of that is not overwhelming with the encounters, but do to the pvp fact, I stay away from San Fran, and the Boneyard areas, and pretty much Mari-Navarro area, cause the gear required to explore there is too expensive for me to want to give up to the random pvp'r who comes in drugged up and looking for lawlz.