Why a hit to happiness? Considering the player does alot to help out, I'd expect settlers would be happy he's settling down there and not somewhere else. Especially later game when player becomes an OP power-armored combat beast whose mere "they live there" fact make raiders think twice about attacking the place.
If player hero settled down in my settlement I'd be pretty happy and feel more secure, after all if the settlement gets attacked that's their house that'd get torched if they don't come help. I mean, maybe if they get a sprawling mansion while the plebs get shacks I'd be an unhappy settler but otherwise its all good. Houses usually cost power, water, etc so that would be a cost to the commune/settlement. Maybe a house that employs a maid or butler would cost the workbench caps somehow, mitigated from taxes or however those caps keep coming into my workbench.
By the logic of the whole "everyone in the settlement deserves water, a home, a job, food and happiness" then that should also apply to the player as well, philosophically.