Um, they're not objectively the good guys in 4. You know that, right? Sure, they're one of the factions the game says are the good guys, but they're pretty openly racist towards Ghouls, Super Mutants and Synths especially, to the point of basically wanting to commit genocide against the last one, so you can't say they're these "humanizing ultimate good guys" when they most certainly aren't in 4.

Hell, you can even go ahead and make them your enemies depending on what you do in the story, in which case you end up wiping them out with Artillery Fire (Minutemen), infiltrating their ship and blowing them up from the inside (Railroad) or turning their own weapon against them (Institute).