I've read this about 5 times and I'm not sure I exactly understand what McL is telling you, but let me make a stab. They may be concerned with the counterbore in the flywheel that accepts the shank of the clutch bolt. If this shoulder were to bottom out in the hole before the cover was tight, the clutch might not draw down completely.
The other holes in the fw are probably for a standard 3/8 clutch bolt, and these typically have a .250" drive shank at the top of the bolt which the pressure plate drives against. Again, this shank has to fit in the hole recess, that is probably why it looks like the threads don't come all the way up.
The bigger issue here in my mind is the moving of the clutch .030 away from the release bearing. You may have to use a bearing shim to make up for this so you get complete clutch release.
Hope this helps somewhat.