When potting up tomatoes, the standard practice is to pot them deeper than they were before.
What about peppers? Do you deepen them up?
I've read that it is a bad idea to plant fruit trees any deeper, as it can cause disease. (peach trees)
I usually plant peppers deeper as I do the toms.
I repot every thing deeper except trees. They develop more roots.
I repot everything deeper and so far have not had any stems rot.