So for Fallout 4: I'm not terribly far into the game, but I'm wondering about how independent the companions are from their respective factions, in terms of the player's relationship with them. Some are very closely affiliated with a major faction (Danse, Preston) so will choosing to side with another faction eliminate my chance to have them as a companion/have a relationship with them?

Thanks!

Well so far, I'm a member of the Minutemen and the BoS. Danse is currently my companion and he really likes me. He even helps out defending settlements, when we need to. So far, he hasn't said anything negatively and even remarked on the Minutemen's honor when we headed to the Castle. He also liked it, when I talked to one of my settlers and told them that I would help out (clearing out ghouls).

I am not far into the BoS faction quest, so I don't know if at some point I have to choose. One of my settlements is also now controlled by the BoS (they needed food resources) and Preston never mentioned it.

Now, when I get started on the Railroad quest line, I think I rather leave Danse "at home", since I don't want to negatively affect my relationship with him and I don't know how he would feel about aiding Synth (at least right now, haven't gone far into his personal quest either yet).

Short answer: yes. Without spoiling to much here but if you make a faction hostile to you those companions affiliated with those factions will become hostile too. Don't know if how much they like you makes a difference or if it can be avoided but I can say for sure some companions will turn hostile.

There are 3 companions strictly related to their faction, and you can lose them according to your decisions, but they won't turn to you until you become enemy of their faction.

Don't worry about Preston.

You can take him wherever you want

Oh really? That's good to know! Thanks!

Don't take X6-88 to the Railroad HQ tho... that got ugly.

So let's say I have recruited a bunch of companions in the past, and they all are chilling in Sanctuary together. And then I make one of them mad at me because I have made their faction hostile. Will they start trying to kill me if I go back to Sanctuary? Will they kill any other settlers that happen to be in Sanctuary at the time? Or do they just leave Sanctuary and go back to their "home," and just fight me if I find them there? Also, are they still marked "essential" (in other words, invincible) once they become hostile, or can you kill them?

Yes, they try to kill you, at least 2 of the 3 companions that are faction related (you can made one not hostile to you, but you lose him as companion).

No, once they are hostile to you they lose their "essential" mark, so you can kill them. Also they start attacking you, but your other settlers can star shooting him.

Note that while you can lose them as companions, you won't lose their perks, if you manage to get their max affinity while you have the opportunity.