Unless the Origin stories are long and very different from each other, that would be even worse than what they did in Original Sin II.
Why whould they need to?
I mean, look what quests we have right now:
- One is helping Minthara slaughter the groove ... and other is helping Halsin slaughter the Goblin leaders ...
- One is helping Kagha drive out Tieflings ... and other is helping Zevlor get rid of Kagha (no matter how) ...
- One is helping Karlach against so called Paladins ... and other is helping so called Paladins against Karlach ...
And lots and lots things is happening around.
From this i say we can expect that our companions would have their own quests ...
They would all be happening in same space (Baldur's Gate specificly i bet), and it would be changing based on wich one you pick ... just the same as it does right now.
Just examples out of my head, feel free to see this as Wild Speculation:
You pick Gale ... you go to Baldur's Gate to search for some magical way to cure his Nethereese orb.
You pick Astarion ... you go to Baldur's Gate to search for Cazador.
You pick Shadowheart ... you go to Baldur's Gate to search for Sharites.
You pick Lae'zel ... you go to Baldur's Gate to search for Shadowheart's artefact, bcs Vlaakith wants it back! :)¨
You pick Karlach ... you go to Baldur's Gate to settle her debts, as she said.

You pick Wyll ... no idea

... but maybe you go to Baldur's Gate to somehow resolve his pact with Myzora, or to gain back his Honor ... or maybe, just maybe, we find out in Moonrise Towers that army of the Absolute is allready marching on Baldur's Gate with all that gunpowder they buyed from Zhentarims, and Wyll will go there to protect his city ... or just go there to clean it from True Souls ... w/e
Also, considering that...
Every "solution" to removing the parasites has been a wild-goose chase.
I know ... but i do believe it was only to push us to Moonrise Towers, nobody knows if this one would be the right or not ...
And since both Good and Evil game was pointing us that way, i wish to believe there is some reason behind that.
The game is only supposed to have three acts according to the FAQ.
It mentions "the adventure" not "adventures" in the FAQ.
...I'd say the characters will be stuck with the parasites for a long time, and none of the characters will be leaving without some catalyst.
I mean it would hardly be an "Act 2" if you would keep dealing with the same problems as you did in Act 1. :-/
Therefore i do believe:
Act 1 - Tadpole problem ... (probably temporary) resolved in Moonrise Towers somehow ... notice that i DIDNT say that it will be removed, just the pressing threat of turning into Mind Flayer will be reduced to minimum.
Act 2 - Step aside ... Origin characters problem ... resolved in the city, probably showed that there is much bigger plot than you think at first, probably even show us why those characters were picked for tadpolisation.
Act 3 - Reveal of big bad boss ... killing it ... end.

Not only that, but I think that the context of what was said in the FAQ makes the meaning of the words abundantly clear.
"Is your party permanent or can you change members out throughout the adventure?
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."
Yes i heard this many times before and it didnt convinced me ... mo matter how much bold or underline you use.

I cant help the feeling that if Larian would like to say us that our party will be permanent after Act 1 ... its nothing easier, and clearer than simply telling us. "your party will be permanent after Act 1".

But they didnt do that ...
So i would like to believe that there is some message we are missing here.
The question deals with being able to swap members in and out of the party throughout the adventure.
Right after saying that you can swap companions in and out of the party, it says "however", meaning that what's said after is contrasting with the previous statement.
The only difference here i see is that you seem to believe you will not be able to switch your party since this option will be simply removed and nothing else will change.
I believe that this option will be present, but you will no longer be able to switch between those companions ... since you loose every Origin companion, except that one you commit to.

After all, remember that Larian promissed us mercenaries ...
It would not have much reason to have Mercenaries, if you dont have a option to take them with you since "your party is locked".

What makes you think that we will deal with the parasite in act1? Parasites are on which every narrative/mechanic contrivance lies. they are not going away - that’s an easy bet.
Multiple things i listed abowe and elsewhere ...
- Everyone is pointing at Moonrise Towers ... Minthara, Halsin, Volo, that Zhentarim vendor in Goblin camp, every single Goblin that is talking about it, Duergars, Florrick ... and i bet i forget someone.
- All other solutions was like "sure i can help you, for a prize" ... but this one is more like "this is where all is happening, if you can find your solution ... it will be there".
- Plus ... and that is also important, they all were thinking they are dealing with regular tadpole ... at Moonrise Towers, we would probably be right by source of this problem.
- We also know, i mean Swen told us some time ago, that all companions were created in pairs ... meaning every companion have other companion that will be somehow important for him ... so far the only pair that is obvious is Shadowheart and Lae'zel ... that also makes me believe that our Origin characters will have important role in Act 2 story.

Also i never sid we will "get rid of the parasite" ... i just presume our problems with it will be resolved.
Meaning we will probably no longer have to fear that we could turn any moment.

I mean some Nethereese magic is keeping our parasite from turning us right now ... i believe all we need to do is to change this from "curetnly in stasis" to "permanently in stasis".

But! Even if we get indeed rid of our parasite ...
I believe that in Act 2 or maybe 3 ... we find out that all that time we spend with it in our head changed us, and we still will have to fight the Absolute.
I would expect something more along the lines of characters not in our party at the end of the act1 to be taken under Absolutes control, or something like that.
Its possible ...
But since so many people allready expressed their concerns about this scenario, i dont believe that Larian would make the same misstake twice.