Having committed myself to an Institute playthrough and becoming Director of the Institute I thought to myself "Wouldn't it be better for the Institute to interact with the Commonwealth by using the MIT Ruins as a settlement location?" This would allow the Institute to trade for goods that they need and recruit outside talent when they feel the need to. The quest "Nuclear Family" would have to be completed as a prerequisite condition since I doubt Shaun would be open to the idea.
I realise that the Fusion City mod allows the player to encourage the Institute to interact with the Commonwealth but ends up turning the Institute into a nightclub that anyone can enter. That kind of solution always felt unrealistic to me so I looked for a mod which would turn the MIT ruins into a settlement location. Unfortunately there hasn't been a mod made for that yet. So here I am throwing that idea out there hoping that someone will pick up on it.
Obviously the Sentry bots patrolling the exterior would have to be removed as well as the Supermutants in the ruin's interior area. I think that only the exterior area needs to be used as a settlement. The interior area would only need the supermutants removed and maybe allow the player to tidy up inside using the same build options that we get when we purchased the house in Diamond City without turning that area into part of the settlement. I would recommend leaving the synths and Coursers that were fighting the supermutants as they would want to restrict access against unwanted visitors.
Anyway I hope that someone takes on this request as it could be one of the few ways that show the player making changes to the Institute after becoming Director.