Nursery overpruned root on bareroot trees

Would that practice create complications for their future?

Bare roots already have severe issues because any sort of natural tap root is destroyed, there's multiple points of disease entry (damaged stems and roots). So, yeah, bare roots aren't as good as seeds in that way. However, unlike seeds you can see a bare root tree, may get fruit a little sooner, and know the variety. That all said, I have a friend who says bare root is the best and I've done them for things I can't get seed for locally.