Need some help with bed rack and tonneau cover

So, I pulled the trigger on a KB Voodoo bed rack yesterday, and I got to looking at the bed rails and mounting hardware for my bed cover. It looks like I won't have the room on the bed rail with the existing tonneau brackets to accommodate the 46" wide rack. Hopefully that makes sense.

The hardware for the tonneau looks nearly twice as wide as it needs to be for the latch, so I was thinking I could either get some T-nuts and rig up some new, narrower latches, or possibly tie the latches into the bed rack brackets somehow. Any suggestions?
I don't have the rack yet, so it may not turn to be an issue at all, but from what I can tell by looking at it and measuring it, I'm likely gonna have to do some finagling... that or swap the cover for the rack every time I want to use one or the other.

Thanks for any help.
The cover is a Rugged Cover II on a 5ft bed. (sorry about the pics, not sure why they turned sideways)