WN's YT "service" does absolutely nothing for the parent / kid and is simply designed to make you aware that you are 100% responsible and that the kid is 100% on her own. I wouldn't bother registering and filling out the forms.

An average 16 YOA is more than old enough to travel alone. If yours is, that's great. If she's not, then she shouldn't travel alone.

Do bear in mind that because BOS-PHX requires a change and because there is always a risk of a misconnect that she needs to have a mobile, a CC and some plans for what to do if she gets stuck at the connection point. Because she can't stay at a hotel alone, I would choose a connection point where you've got relatives / friends who could, in a true emergency (bear in mind that this is extremely unlikely) pick her up at the airport for an overnight.

Only you can assess your daughter's maturity. Most teenager's treasure this sort of thing.