Fan screws are self tapping and do cut the thread into the fan holes. I did think you meant the scews where to big to go through the rails.
I have only used fans in the roof when using a radiator, my build at the moment only has 2 x front and 1 x rear fans.
Out of interest, what is the spec of your PC?
Ah tbh at first I wasn't sure myself if it was the holes or case.
I've gone for air cooling all around, something about water near electrics just bugs me even if it is more efficient.
Once it's all in it'll be 7800X3D, X670 Lightning, 7900XTX, Deepcool Assassin 4, 4TB P3 Plus and assorted HDDs in a C33 commander (2x200mm front fans, 1x120mm rear, 2x140mm top). Might be overkill on the cooling but currently in an 'office' room that gets pretty damn toasty so for a few extra £s decided it was worth it.