Stock covers are pretty dang rigid, except of course the gasket rails when guys herk the bolts down like they're main caps.
Another interference spot I've experienced was at the shaft hold-downs at the ends.
That and roller rocker clearance is what led me to make the VC spacers, but I couldn't sell enough of 'em to afford making them.
I'd prefer denting the baffles to drilling them, if possible: dents don't create metal debris or slivers that can break off later.
Just cradle the VC & use a punch.