In regards to the gap for the top, I'm not sure how it would work with the EB, but I've spoken to the two gentlemen who've had them on their Broncos and asked about leaking around the rear of the cab - considering that over the rails would be raised by the height of the steel bracket.
If I recall correctly, he told me that the gap was minimal, and that the weatherstripping was thick enough to keep water out. However, there is also a lip in that area that even if you didn't get a good seal, the water would hit the lip and run to either side of the truck.
I thought that there would be massive gaps, but I was overestimating the thickness of the bracket plate at the top of the rail.
While I am no where near being ready to fabricate one of these, I plan to so that I have a little extra storage and can slide my hardtop and softop on and off as I wished, without having to disassemble the half the truck. I was also considering modifying the design a bit, and extending the rack area to reach the top of the windshield (at least on the FSB - we'll see about the EB) which then gives me a place to mount roof lights, and an anchor point for limb risers should I go that way. It will also give more stability for when I have to mount my fishing kayak up there.