Seating below the neck/shoulder junction can be bad for any bullet. Most FB bullets are about .0005 bigger at the base than the shank, and that can make a bullet fit the bore tight enough to make a difference.
How is the having the base of the bullet below the neck shoulder junction bad? And what difference does it make that the base of a FB buillet is 0.0005" larger than the shank (assuming that is necessarily so), since the whole thing is going down the bore anyway one way or another?
Because the doughnut that forms at that spot can make pressures erratic and affect accuracy. You can use a reamer to get rid of it, or run the cases back through a case neck turner after it has been run over a mandrel.
You answered your own question with my comment. It makes the bullet fit tighter in the bore. Loose bores and bullets don't shoot very well.
