I got the same answer from vans. The hole in question is NOT an alignment hole. It does line up with a hole on the spar, but the flanges in the rear spar are a snug enough fit with F-01412 that the hole lines up anyway.
here is the quote from an email from Vans:
"I clarified with Engineering to go ahead a CSK and rivet that one hole the same as the rest of them on the VS-410PP. There will be a plans revision forthcoming. Thanks for bringing this to our attention..."
EAA Chapter 1093 member
RV-14 (serial number 140073)
N73XP (at least that # reserved now)