Recruited companions will be at camp when not in the adventuring party, and can be swapped in and out at camp. After the first act however you are going to have to commit, also just like in real life.
I hate this obsession with "real life" as if we're all expecting real life logic in our video games. It was the same with "Why are the companions assholes all the time?" So many answers were "Well, if you had a tadpole in your brain, wouldn't you be pissed???" as if that answers the question in a video game setting.
I don't care that it's "realistic" that my companions don't want to sit around at my camp while I'm away adventuring, I want them to be accessible when I want them to be accessible. They're not real people with feelings lol. I get that they're going with a "replay the story to see how it could have been different", but the kind of person that's going to replay the entire game from scratch is generally the same type of person that would replay the game from scratch if they had all characters accessible all the time anyways. You're not going to get most people to replay the game by locking them out of content.
Because they don't know what's going to happen to them if they don't get their dilemma sorted out? Did I miss an update where the only one that knows about the tadpole, or what it does is the PC?
That said, I'm not a fan of dropping them at the end of the chapter. Although, I'm not sure how I'd write them progressing through whatever they go through to get to the "other side". Maybe an ME Citadel DLC solution, where it's "All hands on deck" thing, at least, that would be the easiest way, although combat would be a total pain to balance/manage. I'm not a fan of "Well, they just hang out in camp, and trust that, despite practically ignoring them for the entire time, we're going to help them too" scenario.