So I just beat the game with the BoS (again) and was planning on playing some more, however the whole settlement management has gotten way out of hand, so I had a thought. What if I do those missions for the BoS where I take over settlements for the BoS? If they go under BoS control will I still get 'Under Attack' and 'Kidnapping' missions from them?

I really don't need supplies anymore myself so losing control of them isn't really an issue. As long as I don't lose Red Rocket of course, my home base. No one there but me and my stuff.

Thanks.

I don't think you're really taking over the settlements, just convincing them to hand over some of their supplies. If you're a dike and threaten them they will do it but they'll also stop being an allied settlement. So in a way you get what you want.