I completed BOS main quest and, unlike the ragtag Railroad and Minutemen, they are well organized and powerful. I'm wondering why they didn't use something else than the Institute's main reactor to destroy them, they could have wiped all their security and locked the remainder, then places a bunch of nukes (either mini or Mark 28) in weak places (or weakened as there would be plenty of time to prepare a demolition) and recover the reactor. Doctor Madison Li and Professor Scara are pretty smart and could make some remote-controlled robot, similar to a bomb disposal vehicle, to bring the Institute's main reactor underneath the hole made by Liberty Prime then hoisted out.
With such a powerful reactor, they could create a complex defended by a battery of heavy lasers which includes a hangar, to make large constructions, as well as large quantities of food and purified water to help wastelanders and settlers.
Optionally, to do such a mission the Sole Survivor could recruit factions not hostile to BOS and even gunners, using a combination of persuasion, advance payment, and share of the output produced by the Institute's main reactor (ie with hard check the gunners could be hired for 5000 caps and 10% of the output). Perhaps also if the total share to be given is under a certain portion (ie < 1/2), the Sole Survivor will be able to access a drop-box with an amount of output invertly proportional to what was expected to be shared (ie the "savings" is split 40-60 with the BOS).