What would cause this weird bearing wear?

I'm sure more experience will come. I'll ad this though.
I wouldn't be surprised on the mismatch from factory. But then, unless you've had the engine since manufactured, you likely don't know if the caps are original to the block I'd think.
It doesn't sound as though you are seeing or feeling rotation resistance due to the condition.
When you say "like one side I can catch my finger nail while I can't on the other" do you mean front to back or cylinder bank to cylinder bank?
Do the caps or block have corner breaks that can enhance the issue?
Did your main bolts turn in straight or wobble as you ran them down?
You could try to reset the caps. It may just end up the same, split the difference, or even move the offset to the opposite side.
The thrust bearing will control the cranks fore and aft motion.