Gonna have to redo a previous save to get all 3 factions. My end game had minutemen & BOS as the only factions left. Also spoke to Maxson afterwards & BOS still turned out friendly even if I killed Dr. Didn't think much of it but it turns out that this will piss off the Railroad & make them turn hostile when speaking to their leader after nuclear option. Once back again at the institute, I didn't issue the optional evacuation order. Li but I ignored it & instead proceeded to do the castle quest then nuclear option. A BOS quest prompted me to go to Maxson once I killed Dr. Li (fun encounter when heading for the exit: huge hoard of synths waiting at teleporter room). First time I got inside the institute, I accepted to be part of it after speaking to Father (to gain access to all rooms) then proceeded to immediately massacre him & the entire institute, including Dr. Did lots of minutemen quests, no RR quests (only intro, main quest involvement), a few BOS quests (up until promoted as a knight).