Yes, the hole in the motherboard tray could be made larger but I am going to leave it alone. The tray is heavy duty steel. I don't normally change cpu's and heatsinks anyway. I have drilled blow holes in the top of cases in the past.
However, I have been thinking about some other mods. When I was at Fry's I saw flexible plastic tubing. They had flexible tubing that looked like shiny chrome and it was available in several diameters. There is a lot of room between the front of the motherboard and the back of the drive cages. I might get a large one for the SATA cables. Just run it down the motherboard tray, along the bottom of the case over to the SATA headers on the motherboard. Maybe do the same thing for the 24 pin power cable. Might give it a nice futuristic look.