I have a case that looks completely different on top, but I made the back foot as one long edge that touches the desk at an angle like your design.
I cut a groove in the centre for the USB cable. After plugging the cable, I covered it in U-profile rubber edge trim, specifically
this one (The page is in Swedish, but there is an image) from a local store that specialises in rubber products. You should be able to find something similar in your town or on eBay. I also cut a smaller groove in the U-trim - and with the cable in there I think that should prevent the trim from sliding sideways.
Your design looks too flat. If you plan to build the bulk of the case of flat layers with cut holes in them, then you would need at least three layers: one layer for the plate, one layer for giving room inside and one bottom. Don't underestimate the space you will need for the switch pins or the controller.
You could perhaps give the controller even more room by cutting off parts of the top plate that will be covered by the L-bracket.