A wipe-on poly should go on so thin that this is unlikely to be a significant issue.
It would probably be easier to not worry about it during applicatono, and then use a pencil wrapped in sandpaper to gently clean up the tuner holes. If you're laying it on so wet that your truss rod access hole is in danger of being occluded, back off a little. It's wipe-on, not slather-on.