Wow that is a lot of play. Have you pulled them out yet to see if there is a bushing or anything that is worn out?
As far as the holes go, It would not surprise me that someone drill them! I have worked with people that would drill a hole like that just because they were to lazy to walk back to the shop to get a shaft collar. So... If it involved getting in a car and driving to town, My guess is they opted to drill instead.
"I have worked with people that would drill a hole like that just because they were to lazy to walk back to the shop to get a shaft collar", a shovel to the back of the head will take care of this kind of laziness. That doesn't even make sense, they would they have to walk to get the drill motor, and these holes if drilled were done on a drill press, no moron with a drill punched through these while they were on the tractor. I would bet my bottom dollar that these holes are either factory OR someone took the entire spindle off and put it into a jig on drill press, way too clean and exact. That part really doesn't matter and I could care less, I googled this question and several others have asked the same thing, clear back to 09, with no real answer on three different forums, weird. Two also mentioned holes and roll pins, somehow I'm feeling some of these manuals may be a little generic. I've read 10 complete parts and repair manuals tonight, I'll figure it out after I get the axle apart, and let you know. I do know the spindle steel is way harder than the cast iron axle, I also know that I can have axle drilled and bushed. i guess that about takes care of it. Thanks