I pretty much do the same thing. Uniform my primer pockets and use my co-ax press too set the primer to get a consistent seating depth for a .002 crush.
Question for you: I use the same uniforming tool to clean the pockets and find I get a little bit of brass shavings and a shinny pocket. This indicates to me that after firing, the bottom of pocket moved due to the pressure. Have you found this to be so too?
I firing stiff loads can make the primers so loose they fall out of corse the pocket dimensions are changing.