I agree with Ruki as well. If we imagine this actually getting spun off into a whole show with seasonal arcs, then spending an entire act focusing just on the trolls with no humans at all probably isn't gunna cut it in episodic form the way it works in the webcomic, so it makes a lot of sense to introduce the trolls as the early acts are in progress. As others have pointed out, the trolls revealing they've been fucking with the kids for YEARS already makes them a pretty easy fit into any part of the comic anyway. An adaptation shouldn't have to worry about hitting all the same twists as the source material, and treating the trolls as twist characters in 2025 out of life devotion to copying the comic 1:1 would be a little silly.

I also think if the cartoon wants to treat Jack Noir as a real arc villain it makes a lot of sense to have the trolls start talking about that earlier on than they do in the comic.