I had every intention of using one of my older PC cases for my last build. But after mounting the cooler (Hyper 212 EVO) I looked at it and thought that there might be clearance issues with the cooler backplate and the MB tray not having the cutout. I thought it looked as if the backplate would come in contact with the MB tray or even press against it, and I didn't want to risk that, so I ended up purchsing a new case with a MB cutout to use for the build instead.
Does the backplate on the Hyper 212 EVO protrude any more than average? I'm pretty happy with that cooler (I swapped the fan) and might like to use one for my next build if it will fit in my old case.
To see if the cooler backplate is too high I'd try sitting the board on the tray and seeing it the screw holes touch the standoffs. But I doubt the cooler backplate would touch let alone push on the tray, someone correct me if I'm wrong but it seems to me the standard MB standoff is 9mm (3/8"), at least mine is and it's a pretty old case. For comparison that's 7 optical discs stacked on top of each other, any cooler that needed that much of a backplate would probably snap your motherboard regardless.