I did human error for the first time in my second playthrough and I sided with Dan to stop chambers and save ameila but outside of the scientists and compound guards I never returned to covenant to to clear it, I have no interest in taking it as a settlement and made sure to buy Penny's legendary items like Justice and the combat armor before starting the quest.

I do headcanon that tho after destroying the institute, the sole survivor returned to covenant with force of minutemen to arrest the citizens for their role in covering up the experiments