This has been plaguing me for a while, finally fixed it.. maybe this will help someone else.

I'd been using the primer pocket uniformer on my case prep station, but still had an occasional primer that didn't seat flush (or a little under).  I went looking for a new uniformer and saw that a few companies make some that are adjustable (RCBS, K&M, Hornady at least), so I got the K&M.. It seemed to miss a few too before I adjusted it.  Found a piece of paper that was ~2thou and poked a hole in it.  Loosened the retainer screw a little and pulled the cutter head out a bit.  Stuck the paper/hole over the cutter head and used a previously uniformed case to set the depth.  So the paper added about 2 thou to what it was.  Tightened the set screw (removed the paper), and all is well in the world.  Loaded about 50 with no high primers.

I use a hand primer so I can feel when they are bottoming out....

Nicely done and well thought out.

As a career machinist, tool maker and related trades it's refreshing to see people taking a true technical approach to reloading.

Motor

I got some Winchester 45 acp that some of the lot had shallow pockets

I have some brass whose case head is a little concave.  It's not a lot, probably just a few thou but you can easily see the cupping with your eye.  Cupped cases are the bane of most uniformers because the uniformer is stopped by the high outer edge before the cutter reaches the full depth of the primer pocket.

The primer seaters don't index off the high edge, so that's not a problem.  The case rides on the bolt face on those same high spots, so there shouldn't be a safety problem.

Still, I don't like cupped cases.

My issue is with the primer sticking up even 1 thou above flush, it screws up my base-ogive measurement..

Excellent concept for fine tuning the adjustment.