Here are black screws:
http://en.mdpc-x.com/mdpc-mounting/screws.htm
http://www.chilledpc.co.uk/shop/index.php?cPath=60_146

I don't recommend switching rivets to making your own threads, the plate is probably thin and that's one reason they used rivets in the first place.
Just buy a rivet tool, they are pretty cheap and then you get, IIRC, 3mm rivets, both flat and round head.

Check my build log how to remove rivets.

MDPC have black rivets but think those are round headed. You can probably paint those with a small brush after they are applied to the case.