I rarely worry about it. I've made about 30 quilt tops so far this year, and have quilted about half of them and have not had it cause me any problems. I suppose if I was making a quilt I hoped to win awards with, this might be something that would cause a problem.
Since I put the plastic template on the front of my machine, I rarely have the problem of the seam catching on the needle plate and flipping that way.