It appears that the fate of each of these companions is tied to the fate of his faction... Is this accurate, especially in the case of Danse and Preston?

Deacon - You must side with the Railroad to keep him as a companion. (Don't want to add spoilers, so leaving the statement at that.)

Danse - You must side with the BOS to keep him as a companion. (There's more to this, but again, I don't want to put spoilers here.) Can you do his Blind Betrayal Quest without siding with the BOS?

Preston Garvey - Do you need to side with the Minutemen to get him as a companion? In a game where I did, I was able to get him after the ending sequence. I'm now playing a game where I sided with the Institute, and he just gives me Minutemen quests. Not sure if this is a bug.

X6-88 - I'm assuming his fate is tied to the Institute's.

it is difficult to answer any of this without spoilers... but trying to be vague... your faction chose do seem to impact some and not others...

Personally I wish you companion choices came with more consequences and the companions interacted more than just making comments at each other when you swap them out...

It is weird wandering around everywhere with Strong without anyone making comments when they should be running away screaming and/or shooting at us...

Though in other cases this is implemented logically. Try visiting the RR with X6-88 in tow..

As long as you don't go too far in certain questlines, you can use all of them. But there is a point of no return for some of these companions. You'll know when you get there.

I don't have a problem with this. If you want a companion's "bonus" just hang out with him/her/it before you go too far in certain questlines.

I've got some comments from the guards in Diamond city when I've visited it with any nonstandard human companions. I find it a bit silly that they don't kick some companions out but then again I guess that could easily get too agravating to people who're not that heavily vested in the story side of the game.