Kadie, It depends with the seedlings, what size they are? I am of the mind that you are best to take cuttings for scions from your new trees once they have started growing. Seems most make the statement that one should wait on bare root/leaves stripped trees, until actively growing.
After saying this. Rinoa had posted on her FB page about shipping cost and asked people to comment. Her question was. Do people mind if she prunes the branches, if necessary to fit in shipping box, rather than having to go with a larger box. Then increasing cost of shipping.
So, here she will be pruning off bare rooted trees?
I find that I go outside of the box, sorta speak with a lot of stuff.