Regarding Companion Relationships and the Main Quest [No Spoilers]

Just a quick question for anybody who's progressed far enough in the main quest to know: Assuming I don't actually have my companions travelling with me, will my decision of who to side with in the main quest affect how my companions feel about me? Obviously, I imagine it'll have serious impacts with companions like Danse and Deacon, but what about more neutral companions, such as Piper, Nick, Curie, etc? Will the main quest affect their affinity levels if I don't have them with me at the time?