Like many hear I'm confused regarding the question of comfort: your daughter's size is similar to many adults who sit perfectly fine. The question of comfort is more linked to the fact that airplane seats, in Y, are simply uncomfortable, irrespective of size :-)
What puzzles me is the OP's insistence that using the car seat would be safer for his daughter of near adult size. He refers to her as short and light for her age, but the numbers he gives,
4'11" 88lb 12 year old, are 50th percentile for her age, not excessively small at all. In the case of an emergency evacuation, I would expect the car seat with a shoulder harness to be an impediment to a fast exit by someone that barely fits in it, and a bulky obstacle to get around.