I got a MK5 on a 20 MOA cant rail and rings. No issues getting to a 100yd zero with bottoming the Elevation dial on initial setup.
I think I have like 1 MIL that I can go down with the dial. It's been too long since I messed with it.
So I'd expect your rifle rail to be 20 MOA along the scope mount at 0 MOA. It's not any real difference at that point. That would tell me your scope isn't dialed as low as possible. Some of your posts read like you removed the caps, but I just didn't read it that way.
The caps have to be completely off. Flat tip screwdriver, coin, or whatever fits run the Elevation internals all the way Down. Be careful at the bottom. It feels like it's almost there (like one click left). Put the cap on, tighten the set screws. Bring the Elevation Up 10 MIL (should be about one full turn of the cap). Now set the Zero Stop as the manual states. This should give you a baseline to get on paper, then adjust the dials as needed. If you need more Down, the Zero Stop doesn need to be depressed. After you are happy, set the caps as you want.