Yes, its ok for him to sleep on his tummy. If this is a new skill, his naps may go wonky too. I use safe-t-sleep, which keeps mine on her back and will take it away when she learns to roll over the other way (i did the same with dd1 and 2). I would try and resettle him on his tummy rather than flipping him back every time so that he gets used to sleeping on his tummy and in different positions.,...and make sure he gets plenty of opportunity to roll during his A time so that the novelty wares off.
With regards to the short morning nap, it could have been a one off or it may be that he wasn't tired enough to sleep longer (needing more A time) or it may be the rolling over.