Is this how you grow your seedlings? Do they survive? Let's see a pic?
OP let the seedling grow for another three weeks or more and don't disturb the rootball till then or it may break apart and you could lose it. Then move it into a bigger pot. Does the pot it's in now have drainage holes? And don't feed it for another two weeks. Then start with a weak solution.
Yes bury them up to cots it saves a few inches. The stem will begin to form roots and have a hw another root ball. Closet offered good advice. What's so odd about it Danny? Its a common practice to save height especially upon micro grows. There's even a sticky on it. As far repotting I would go based on time id look at drain holes and when you see roots guve it two more days and transplant for a tighter structure and less chance of damaging the ball.