I decided to weld up my hardtop holes so I used some knock-out slugs to back up the holes while welding them closed. This will allow weld to be strong and get a good deal of penetration so that when I grind them flush the weld won't be ground away.
When I coat the tub with bedliner, I will put a good coating over the slugs on the inside so they don't stick out and snag anything.