I'm finding it difficult to believe there is THAT much difference between different focusers. It's quite a significant difference to be able to see on print and have an agreement between two people.
Going 35mm (I am assuming) neg to 12x16 isn't all that unusual.
I wonder if there is another factor involved. Say you focus carefully with a grain focuser. The focusing stage could drift a bit and the image goes out of focus. Something like that? Can you carefully focus the image with one focuser. Let it sit there for 30 seconds or so then look again. Is it still in focus?
It is true the DOF at base board is quite big. But the focuser is used to adjust the distance between film stage and the lens stage. This adjustment is quite critical.
I'm amazed you can actually do better with your naked eyes. I cannot. Not even close.