The flash holes are enlarged in blank and 'wax' bullet loads to avoid the primer set back and cylinder lock-up problems.

I would guess that the warning not to use these cases with the oversize flash-hole for normal bulleted loads is simply from todays businesses being extra CYA about things.
The flash-holes being different size from what is normally punched into cartridge brass, they are just trying to protect themselves should anything happen.
'We Told You Not To..'

I used to have a few boxes of 38spc that I drilled the flash holes out for wax bullets.
After the novelty wore off, I dumped the altered cases back in with the rest of my meager supply at the time and continued to load and shoot them.
They worked fine. I loaded just light B/E match type loads. Never had a problem.
But I don't know what effect the altered flashhole would have with heavier loads.