I'm aware of the fact that "Legion Assassins seek your head as a trophy for aiding the legions enemies" in the case of NCR, but how do they react to Mr. House and Yes Man? The entire point of my newest playthrough is so I could leave the fort alive and keep my Legion fame, but if I automatically become an enemy after doing enough quests for Mr. House, it's pointless.

Does anyone know how the quest works in terms of Yes Man/House?

I know for a fact that if you do Mr. House then they come after you, but you might be able to get around that with a high CL rep, not sure about indy playthroughs but I think the same applies.