As I said, I think you're just confused on how zeroing and co witness with a pistol dot works.
Just because you're adjusting the dot one way or the other, you STILL want to put the dot center of the glass. There's no circumstance that you should have a "zerod" dot that you're aiming with at the bottom of the glass. lol
Co witness sights have absolutely nothing to do with it. They're irrelevant to your dot zero. If you have a lower 1/3 co witness the dot will sit above the sights. You don't try to manipulate things so you're using the dot at the bottom of the glass so it co witnesses perfectly with the sights.