Obviously there's no way of knowing, but it seems pretty unlikely to me that the tadpole problem will be dealt with by the end of act one. Maybe it could be, but then what would the story be?
Your gues is as good as mine ...
But i would say:
Act 1 - Tadpole ...
Act 2 - Personal quests of Origin characters ...
Act 3 - Final confrontation with big bad wolf.

Because the tadpoles and mindflayers and all that have been built up as the main conflict of the game.
Well, as far as i know Larian specificly told us in one of interviews, that: "You have no idea so far what plot twist we prepared for you. *evil laugh*"

Also, many theoretizing youtubers are quoting some synopsis, where Larian specificly mentioned Dead Three.
So ... who knows?

It's possible that by the end of act one we'll be in a position where we definitely know that ceremorphosis is either not a threat or at least not a short-term threat
Exactly what i would imagine ...
Finish of Act 1: We will be definitely sure that ceremorphosis is no longer a threat ...
Finish of Act 2: We resolve our dedicated companion problem ... and right after, either our Tadpole, or the Absolute him-/her-self will either remind us that our problem actualy was not so resolved as we thinked, or that story of our companions is tied to the Absolute more than we expected ...
And in Act 3: (
since there is not much reasons to describe end game
) We will, now totaly sure that Absolute need to be dealt with once and for all ... start our final crusade. :P
It would be a really weird choice if the tadpoles and, perhaps more specifically, all the problems that the tadpoles bring with them (this business with the Absolute in particular) would just be settled in a way where the characters can move on without concern.
Oh you missunderstand me ...
I see that simmilar to all our chances to remove tadpole in EA ... we will be offered a solution, our hopes keep building more an more ... and once we believe that our problem was finaly resolved, it will kick us back in our teeth.

Only this time, i believe that kick will take a little longer to actualy show.

If you think that's the direction the game is going, I'd love to hear why.
And i hope my answers abowe will satisfy you.

I believe that when Shadowheart told us "we'l be going our separate ways of course" ... when you ask her what will she do after our tadpole will be cured.
That is actualy hint (maybe unintentional) from Larian about what to expect.

I think by missions he just means quests.
Well, since he is not first person who mentioned the word "missions" and usualy people used this word in connection with sending companions that stays in camp to missions, while we will be adventuring around ...
I just felt the urge to express once again, that i cant imagine worse idea.

I don't want to be in a position where I have to choose my long term party based on class composition rather than which characters I actually like. In crpgs I usually take an optimal party when I know I'm going to be facing tough fights, but otherwise I just keep a party full of my favorite characters.
That is entirely different story ...
Maybe i was not explicit enough, but i believe that there are two possibilities.
Either our companions split to two group, where one will be against the other ... or good, and evil ... not sure ... and we shall pick one to acompany.
Or, wich i concider to be more likely ... game will determine companions with wich we will have "enough reputation" ... we will have to decide one ... and everyone else will go their own way.
And since that point, we unlock non-origin companions, wich would make our group from now on.
What makes me think that is mostly the fact that all Origin companions so far (including Karlach) is created so they can follow the exactly same story, as our custom character ... therefore i believe Larian created Origin stories for each Origin character, and our custom character will be just following them in the same way.