I'll be removing the protective plastic. I only left that on so it doesn't get scratched up. However, it does actually work through the protective plastic so it should work even better without it! The bezel itself doesn't interfere with the touchscreen since it only touches at the very edge which I think is a "dead" area not sensitive to touch.

I'm still undecided on hacking up the case or not. I kind of like the idea Trash80 mentioned of cutting out a hole for the I/O shield, but setting it inwards about an inch so the VGA loopback cable doesn't look so obvious. That would also make the whole thing able to sit closer to the wall as all the cables would be more inset as well.