I've just run into a bug I haven't seen published anywhere, at least not that I can find. So I'll lay it out here - not so much as a question, but for information. I think I can work around it to finish the game. I am playing on survival mode, so no standard fast travel is available.
I'm at the point where I am going to choose between the Institute and the Brotherhood. Both Mass Fusion and Spoils of War are active, but I haven't traveled to Mass Fusion through either method yet, nor have I spoken with Allie Filmore about it.
While doing something else, I traveled by vertibird, which took me directly through the Mass Fusion Executive Suite during the flight (at an earlier point in the game, I flew near enough to the Suite in a vertibird, so I had already discovered the location). There was a teleport flash, and the quest objective "Locate the Beryllium Agitator" popped up, but the vertibird flight continued as normal.
Later I go to talk to Allie Filmore, and all I have are generic dialogue options. She won't talk about Mass Fusion, so it appears I can't continue with the quest.....
...but surprisingly, I can use a vertibird grenade and fast travel via vertibird to the Executive Suite. Even though I haven't progressed through the quest objectives, the keycard is spawned, so I can go down the elevator. There are no synths or Brotherhood soldiers while traveling down. Getting to the bottom, there are several Brotherhood soldiers there who thank me for helping destroy all the synths.
I am able to continue with the quest as normal, get the Agitator, and then return to Allie Filmore who is suprised that I managed on my own. Mass Fusion is complete, I am still in good standing with the Brotherhood, and Spoils of War is still active.
I head to the Prydwin and hop on the vertibird to go to Mass Fusion. It warns me that it will piss off the Institute, but I want to see what will happen so I continue. It fails the quest "Pinned" and starts "Banished from the Institute." When landing on the roof of Mass Fusion, it will not complete the quest objective "Jump to Mass Fusion's Roof" and the quest marker remains up there. I already have the key card, so I can go down the elevator, which goes all the way to the first floor, where the Synths ad Brotherhood are still fighting from the first time I was there.
It seems there's no wa to progress in this quest since Mass Fusion was completed. Makes sense I guess, since they're mutually exclusive, I just get to that point a different way. So I will have to reload my earlier save and pick just one quest line and go with it. I'm sure completing the bugged Mass Fusion will still allow me to anger the Brotherhood later.