The most common application for j cradle style kayak racks is to mount one on the driver side and the another on the passenger side. It uses up very little crossbar space and is usually a good solution for factory rack crossbars too, allowing you to mount 2 kayak racks when normally you would only be able to mount one kayak rack onto the factory rack crossbars if the kayak rack is the type that carries the kayak flat.
Also, with a j style kayak rack on either side of the vehicle it makes it very easy to load each kayak. You just lift one end of the kayak up onto one of the j cradles then as you lift the other end of the boat up into the other j cradle its pretty effortless because the j cradle that already has the kayak in it ends up doing the heavy lifting...
So in your case adding a 3rd j cradle kayak rack in the middle does present a couple of challanges. Mostly with loading that 3rd kayak. The plus is that you could get away with 58 inch crossbars instead of 65 inch (Thule load bars) or 66 inch (Yakima bars). If you are comfortable with the balancing act required to slide the kayak into the middle j cradle kayak rack either from the side or from behind then go with it. However, a better solution would probably be to have a j style kayak carrier mounted on both sides of the crossbars and then mount a 3rd flat carrying style kayak rack in the middle. This way you can easily load the boat from the rear of the truck.
In my opinion an excellent system would be the
Thule 430 Tracker II base rack system with 65 inch load bars and the TK Tracker #1 Kits mounted to the tracks already installed on your truck cap shell (as you stated). And then mount one
Thule 883 Glide & Set kayak carrier onto the middle of the bars. Then mount 2 sets of
Thule 835PRO Hull-a-Port kayak racks on both sides of the Thule 883 Glide and Set kayak rack.
FYI, you can mount kayak racks outside of the base rack Towers (with Yakima) and Feet (with Thule). You will still be taking full advantage of the load bearing strength of the cross bars. I wouldn't bother with trying to reverse the cradles to face towards the inside. This really doesnt increase fuel effiency and it makes it much harder to load the boats. Plus the Thule 835PRO j cradles can optionally fold down completely when not in use. This is a very cool feature that avoids any overhead clearance issues and does actually increase fuel efficiency.