I rotate my primers 120 degrees and seat them to the bottom three times. When the thumb lever is bottomed against the tool on three turns and the primer is still high "We have a problem, Houston". The factory punch leaves a ring indented into the surface of the primer because it does not support the primer edge to edge across the face. It is just small enough to hit inside the sides of the primer causing the radius to buckle under the seating pressure. I try for 0.003" - 0.005" below the head but with some case/primer combinations flush is about it.
Just for reference, I have reloaded 100,000's of rounds. I used to shoot machine guns competition in Idaho and a days practice is 1k. When I started reloading in 1971I would shoot 500 rounds every weekend through my S&W M28 and cast bullets and reload my ammo the next week for the following weekend. Even for my progressive press in 45 ACP I hand prime everything.
I got this priming thing down.
KB