Some were OS from factory on my RV-4
My RV-4 kit came with a couple OS holes/bolts in my spar and splice plate from the factory (likely to get an in-spec condition), and were marked as such, with supplied OS bolts. As others have mentioned, all the spar carry through bolts are NAS spec bolts and should have no play at all. they are drilled/reamed to have close tolerance fit and almost interference fit. In your case, depending on edge distance and a few other factors, Van's tech may/may not agree..they have a liability. At my day job of 43 years, I have specialized in this type of work on airliners. You are close by, and I may be able to assist/advise in getting the holes "true and round" to spec as we say. This not a job for a "bigger drill bit" and it will be fine.