Quote Originally Posted by daihashi
I thought if you covered the stem with additional soil at this point it would just cause the stem to rot or something like that.

I believe I read it in a post with stinky or weedhound.
I've never had a problem with adding soil to seedling cups, but I've never had to add literal inches of soil just to level out the container... maybe that's the difference. I'm also careful not to water around the stem, especially if I've added extra soil, and it's always worked out fine for me. Granted, I've only had to do it a couple of times, but I've never had a stem rot because of it.