Using common hex-screws for the motherboard is only problematic if you don't use a rubber between the motherboard and the screw head. The screw hole/area grinding is not a problem since the whole circled area has no circuits in them. Anyways you should always use those hex stands behind the motherboard so using the correct screws with it will still be perfect, even though you forced it a bit.
So you are fine unless it cracked and that is a different story. I doubt it did cracked since I repaired many computers that were using those hex-screws with rubbers and the motherboard was not damaged at all. :-)
Remember do not screw too tight. The perfect tighness is when the motherboard is not jumping anymore while you shake it slowly, no more pressure than that is required to hold the whole thing..
Unless what cracked?
Also, that material is still there for the most part, I'm guessing that means it still serves its purpose to prevent stray EMI? Also, if I was experiencing stray EMI, what might the symptoms be?
Guessing I voided the warranty too :|