It seems the cutouts were a precaution that DeTomaso had in place in case they needed to use a different powertrain. They serve no purpose for our 351C and ZF combination. I have filled them on two Panteras without issue. The engine bay looks nicer without them. Other unused holes can be filled as well.
On the flip side, they are original from the factory and thus stock or stock-ish cars need to retain the holes.
Below is one with the holes filled.