It's a clear disadvantage. She won't be getting the PCS she usually gets when skating in the last group. I think we might see the same thing happening what we saw in last year's Worlds...
Most of them will be the same. Team Event's judges is drawn from the available judges of the individual events. The difference is judges will not alternate for Team Event. Pretty much all of them would be watching every single event, one way or the other so at the end, it really doesn't matter.
Oh, I'm sure they knew. But at the time they could easily have also thought, "Vancouver was over three years ago--who knows what kind of shape she's in now?" Doubts were expected given her long absence.