Twisted Throttle denies compatibility for liability reasons. As you've seen, there are guys on the forum who have installed the SW Motech side and top racks together on their bikes. Personally, I'd go with what guys have actually done rather than worry about what Twisted Throttle says.
I seem to remember a fastener issue with a shared mounting point as well. Not insurmountable, as a longer fastener can be sourced. Ended up going with soft bags instead of the side cases; personal preference.
I have both installed, and had to put a single washer under the rear latch of my seat to keep it up off the brackets. I put the GIVI 35 bracketry on first, then put the alu rack on top of that. It works, but just make sure you use long enough bolts. I bought new ones that fully engage the available threads on the bike. I also used locktite. Another thing to remember is all that stuff you bolt on is load. Make sure you don't go over your load limit with passengers and gear combined.
Check out my youtube channel, korysrides. In the video for the