Future squad members

The Quarian ark still had something between half a year to a year of leeway before the Reaper invasion, and on top of that, the initial post-Khar'shan Reaper invasion essentially beelined for the major homeworlds (Earth, Palaven) and concentrated there. Thessia came later. Rannoch and Tuchanka didn't merit a full Reaper presence, and Sur'Kesh seemingly went ignored. The Quarian Ark could've conceivably left during the initial stages of the Reaper war, and I suspect that the DLC that introduces them will have us fighting leftover Reaper forces that managed to get aboard and partially infest the Ark.

In this regard, they wouldn't have to canonize any particular ending, because they would've left before it'd been decided.

And no, Tali wouldn't be one of the characters aboard the Ark, her simple presence in ME3 aboard the Normandy, provided she survived the suicide mission, precludes this.