I always get the rectangular marks on the primers. It's from the striker channel in Glocks. I have thousands of .40 S&W range brass and I can always spot the ones fired through Glocks by the rectangular mark in the primers. Well, that and the bulged bases. I use a Redding G-RX die to resize before I load them.
I need to shoot some factory .40 S&W through this pistol again to see if I get the same marks on the cases. I took apart the magazine I used and found nothing out of the ordinary.
The primers aren't flattened any. What signs of high pressure are you seeing? Not challenging you on your evaluation, I'm still fairly new to reloading and am wondering what you're looking at.