With a new XL650, after about 1,000 rounds I suddenly had high primers as well. I found two solutions: first, I did as you suggested, and just improved my upstroke to firmly seat the primer.
The second solution was to tighten the shellplate, as Dillon instructs in the troubleshooting section of the manual. My shellplate was a little loose, and I think the brass-tipped setscrew was where the problem started, because it was a bit loose. I removed and cleaned the shell plate and put just a small thin film of Slide Glide (regular) grease along the path on the bottom of the shellplate where it contacts the ball bearing. I tightened the shellplate to where it would not move, then loosened it just enough to get it to rotate smoothly. Then I tightened down the brass-tipped set screw.
The result: no more high primers, and less powder spillage.......
until I loaded about another box of ammo, got sloppy with the upstroke, and then had to concentrate on the upstroke again.
My conclusion: a nice firm shellplate is helpful, but a firm upstroke is vital.
Chris