i have had many mobos installed with i/o shield plates such as the one you mentioned with a spongy back all intalled fine with mobo , you may have to slightly press mobo into the spongy bit when mounting the mobo to line up the standoff holes but this is quite normal
Im having a hard time, the io while matching, the audio output is a lil higher, i fear the case the culprit so im trying to push the metal back a lil so the mobo end up a bit lower. The audio go in fine, but is on the top border
If it all goes through the holes and all your board standoffs line up properly then I don't think there should be a problem. I'm fairly certain that some of my I/O ports look a little off center, but the point was that everything was able to be screwed in properly. Just make sure the shield itself was pushed in properly
I do remember my Sabertooth took a bit of pushing to get things through and lined up right (nothing huge, but it was a bit reluctant at times)