You are an experienced precision shooter and probably know a lot more that I do, so I offer this only as my experience regarding primer pockets. Also, this is offered in the context my shooting discipline, precision varmint and predator hunting.
Over the past 50+ years like many, I have always sought an edge to improve performance. For many years I just cleaned the pockets with an RCBS cleaning tool to remove the gross primer residue. I still believe this is important to obtain flush seating (slightly below the rim of the case).
Seeking improvement, several years ago, after reading many articles, I purchased the Sinclair pocket uniform tool and started uniforming primer pockets. This did an excellent job on most cases, but like you, I experienced some cases where the pockets were a few thousandths deeper, and the tool would only uniform a portion of the pocket.
After years of doing both (i.e., uniform and not uniform) and shooting thousands of practice rounds on target, I can tell you that it has made no difference that I can detect on target.
The one concern I would have with a uniformer that you can vary the depth of cut is that one might cut it too deep thus creating reliable primer ignition problems. So, take this for whatever it is worth.
Take care and Good Shooting.