You are correct , these rivets sit a little proud because of the pro seal between the matting surfaces of the rivet and skin.
A rivet shaver has never worked for me.
What has worked is taking a stiff sanding block, no padding, and sand them all down. You'll end up with a perfect row of rivets and your painter will be very happy. Any part of the rivet that sits proud is doing nothing except ruin the paint job and draw your focus every time you look at your tanks.
Maybe a 320 grit and take it easy when you get close to the skins. A few scratches won't hurt. Your painter will scratch up the whole plane before painting
I would wait a few weeks to let the pro seal thoroughly cure.
RV-8 finished (sold)
RV-10 Flyer 400 plus hours
Over 2500 Gallons of E10 mogas burned
Don't believe everything you know.