So far, I have built the horizontal stabiliser, the elevator, the trim tab, the rudder (and the ICP rudder extension), the fin and all four flaperons.
So far, all the holes have lined up somehow in all of these ten parts. In some cases, they did not initially appear to line up but (in the manner described by Bob above*) I have always managed to line up the holes so that the rivets could join the components.
I would strongly advise that you do not run the drill through any of the the holes to make them fit, but instead, try to make the holes line up with a podger.
* "if it won't stitch together in one direction, try it from the other direction."