Ah, gotcha. Those are under the brackets. I wanted them to stay below so that they could stay tight. On mine they sit slightly below flush. I can add a recess into the mounts to help clear any bolts like yours that may not be flush or below. Thanks for pointing that out.
I have a 500x500x500 machine that should be here by the end of the week. The reason I used the ball mounts on the all thread was to allow angle variances. The 500mm machine is only 50mm taller, which only changes the angle slightly. The ball mount system should be able to account for that, but I will test it as soon as that machine comes in. :) I will definitely have to redesign the triangular brace, but I anticipate all the others will remain the same.