Neither of the slots will share lanes with the GPU, but the M2P_SB is conected through the chipset/southbridge, and will thus share bandwidth with anything else connected to the southbridge. In an ITX build like this, that is likely to be essentially nothing, so the difference will be negligible in that regard. A chipset-connected slot will still never be as fast as a direct CPU connection, but again that's negligible - you'll see it in benchmarks, but you'll never notice in the real world. Unless the boards has some weird BIOS config issues or chipset driver issues, I doubt you'd notice the difference between the two configurations if you tested them side-by-side.
Speaking of cooler mounting: are you sure you won't be able to mount it beforehand? I get that it would be annoying with pre-attached cabling and everything, but it's a pretty straight shot into the case, so it might be doable. If not, then the SecuFirm mounting should still be relatively easily reachable through the cooler - that's how it's designed to be screwed down, including cutouts in the fin stack. You'll need a sufficiently long and thin screw driver to get through the fins and fan blades, but it should be doable.
Btw, if you want to free up even more space in the front, try to find some black plastic somewhere (packaging for something else, whatever) and tape/glue it in inside of the I/O holes instead of the non-functional PCB.
