Your message made it onto the list twice on 26th March (alpines-digest #635).
I also have oversize holes for the lift-the-dot studs on the B-pillar. I bought some studs that have a proper thread and nut on them, instead of the 'self tapper' style thread of the originals. HOWEVER - I haven't been able to find a way inside the panel in order to get the nut to the back of the mounting hole (I must say that I have other priorities so I gave up pretty quickly).
I suspect that the enlarged holes at this location is due to the tonneau cover being too tight, and only one clip (per side) to take the load along the side area.
I know this doesn't help you much, but at least you know you're not alone...
Cheers, Paul.
--