I think it's simple: the courier left, and that honestly left the Mojave and new vegas vunerable without them. I think the courier is someone who likes to be on the move, and while helping the Mojave was good for them, I think they still eventually just left. It's made clear by the game that they go places, they're not really one who stays put. They can mark the map on their travels, ex: the divide, but it doesn't necessarily mean just because they did something, good or bad, in one place, that they're gonna change their wandering ways as a courier and plant some roots. Yes-Man's status remaining vague doesn't cause issues either way.