After the Main Line End - Nuclear Option ?

[jaderive]

Hello, Last night I just finished doing the nuclear option with minute men, also while being allied to railroad , and friendly with brotherhood, made special saves during that time , knowing reponses were coming so I reload and check ouyt what the other reponses were like , that point in the game being first ish play thru, nearly broke my heart, I felt deeply sorry for old shaun, ( took synth saun with me) and really did wish that there was another way=(, I'm someone who'd in the middle of both sides seeing pros n cons of it , but in the end still chose to blow them rather than join and lose all 3 other factions o.o , tho in another playthru I may just go siding with institute just to see how things n such , I've watched a lot of you tubes about the endings and things mid way , I feel sorry for sturges, bethes just turn him into a blank tradeable slate after that, tho prior to doing N O quest he doesnt have much interaction anyway unfortuantely , =/ I've really really enjoyed playing , I didnt like it at first because it was just so different from play skyrim, Im glad you charectar has voiced reponses making it more immersive , love how they have romance option and give you buffs / stats for high like affinity with companions, reminds me of enderal with that part, those of you played that, but after doing nuclear option still have some quest lines and radiant quests to keep me busy and poi places to still discover which is nice , so with all that said , sorry about the min wal of text, I just have a couple of question if somone could let me know please on P,A.M mostly

1 - ( 2 in 1 question ) Pam gives a quest called " clean equation" where I have to kill a BOS scouting duo or such , if I do this quest to which I have reloaded to save knowing she'll give and want to travel with bos a litle more, will it cause everyone on the prydwen to go hostile soon as I get back there ?
And dO I need to do red rockets glare , I really dont want to attack BOS after all this, does pams Clean quest lead to or need this ?

2 - After nuclear quest Ive noticed a lot of Atom Npc's now converging on the commonwealth
I never interacted wtih them much except one for virgil serum quest , and some seem to be siding with raiders, so a new set of bad guys to cope with / play with ??
Thanks !