I'm going to caveat this my saying that I /think/ that precise primer seating is done in an effort to ensure uniformity. I would think that in all but the most extreme circumstances, the difference that would be seen on target is within the margin of error for most shooters; that is to say that, for example, on a good day, I can put up fairly consistent half MOA groups, so anything that would fall within that range isn't going to be noticeable to me.
That said, I recently purchased the 21st Century primer seater, and have decided that the rear of the primer should be as close to the rear of the case as possible (without being proud of it; so flush, or just baaaaarely recessed).
As always, I reserve the right to be wrong...