IIRC, the 6 had an update right before the 6S shipped. When I went to restore my 6S, I had to first set it up as new...update, and then restore from backup. I cannot remember if this is the norm, or if the SE will just ship with 9.3.
Thanks. I think the 6s issue was because an update made it 9.0.1 (or whatever it was at the time). I just need to remember to stay at 9.3 the next few weeks even if there is an update.