RE: Does it matter if you don't kill the boss in the militar
The military base is sort of loose from the rest of the game. It's more of an easter egg then anything else. A reference to Fallout 1 and a little explanation (the holodisks) as the storyline is concerned. If you didn't kill him, you're fine, allthough he has a holodisk on him that is an interesting read. Other then that it doesn't matter if you kill him or not.