I'm not sure... I know you can definitely use weapons you're not supposed to, though. Autocannons are devastating, and the double-plasma rifle is... interesting.
There IS one issue I bring up, if you start a new game with the intention of cheating, and change your spear to something that the starting character model has no animation frames for, the game *Will* crash. I tried to give myself a louisville slugger a dozen times before I caught on to this. Just hold onto it until you've got the vault suit and you should be OK. I'm not sure if this is your "End-boss-gun" problem, though...