Hey Imsofluffy,
damn, you are right. I never had a closer look at this paper since I was not interested in the Rolling folding Stand.
Well, as for the controller attachment, it’s a minimalist design, isn’t it. There could be better ideas on how to implement a better mounting option for the controller, but it would take a little more effort.
How is it supposed to work with the QCW Frame Secure From Above? Now I fully understand your question! 
I think I would try to drill four new holes into the T-track extrusions to mount the controller separately from the wasteboard. And to avoid clashing with the nuts for the secure from above, I would slide small spacers onto the new, shorter bolts to have the controller “hover” them with about 1/4" clearance.