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
Why not? There's no risk of electrical shorts (the Hyper 212's backplate is electrically insulated on both sides, and even if it weren't, most mobos have no exposed traces/components where backplates make contact) so as long as you can screw the mobo to the tray, what's the problem?
And actually, a little contact would be beneficial,
as the tray would become a direct support for the CPU cooler, reducing the risks of the cooler tearing off should your case take a jolt during a move and allowing higher-pressure mounts by preventing the mobo from concaving when the cooler's tightened down.
Regardless, altering standoff height will almost surely make for a great deal of annoyance. Installing expansion cards will be a royal pain and I/O shields are your friend, blocking EMI and preventing you from pushing conductive things into your computer. I've done that several times while blindly groping around the cable tangle sprouting from the back of an unshielded rear panel, and it's pure luck that nothing got shorted.EDIT: Oops. You're worried about contacting the side-panel, right? I'm confident that any case with more than 7.25" between the mobo tray and the side panel should work fine. By my quick-and-dirty measure, my Hyper 212 needs ~7" clearance from tray to heatpipe tips, and a 0.25" safety margin should comfortably accommodate differences in your standoff, CPU, CPU socket, and mobo dimensions.