These are valid points, but I think the main thing overall, is that the Taos fell out of the portal, not flew into the portal. Meaning it probably fell out of another universe, that universe being XB2's universe. I mean the universes were already connected through Klaus anyway, so meh. Portal might be residual Zohar energy, but I don't know
Xenoblade Definitive
Josiah Peterson
Jack Sanders
Nah, I'm pretty sure they explicitly say it's Leftherian wildlife being misplaced when you fight the Jagron.
Carson Hill
Fun Fact: in PxZ2, while she is on Xbc1's world (the fallen arm to be specific), T-ELOS comments that "this place feels like lost Jerusalem".
Jacob Robinson
No, it's Leftheria. It's brought up in the main story with the Jagron fight, then later again in a sidequest.