I don't really follow Osseous's recommendation (maybe referring to tightening the thru bolt?), but I try to keep them fairly close to the sides of the lowpro, I wouldn't say to the mm, but within a few. Access to the ubolt nuts are from the top, so side clearance really doesn't play a factor in tightening the lowpro to the side rail.
I posted the photo below last year showing the whole rig, pardon the strange shape, it was taken from above in panorama mode to get the whole thing in one photo. You will notice I scribed the notches fairly tight and cut some secondary notches to allow access for adding straps. I would cut the access notches a little deeper the next time around (these were cut 1.5" back from the edge as I recall; I'll probably go 2.5 next time). They can still be hard to get your fingers in to grab or push straps under the frame.
Have fun tinkering!