I can vouch for the Yakima tracks working well. I have also used an old style Obsolete Thule tracker foot for a 2000 Dodge Durango from thule. I believe it is the 530. Without the plastic base it is almost flat. Just a tiny angle which matches most caps well. You make a sheet metal backing plate for the inside. Then drill 3 holes for each through the roof and backing plate. Seal with Black polyurethane caulk. This is a permanant but strong mount. On my Titan I used large aluminum angle for the inside backing plate and drilled 3/4" holes in the other flange. This allowed me to put 3/4" PVC pipe throu for curtain rods hanging racks ect.
Look close and you can see the Aluminum angle in the corners. It runs legnth wise 4" long.
Yakima and THule also make brackets that mount on top or on the side of the cap by through bolting for rain gutter mounts. These will allow you to remove the bars.
On my old Powerwagon I used some old Thule cross bars and some 3/8" eye bolts, fender washers, An all thread coupling as a standoff. Put the eye of the bolt inside the truck to tie things to. These eye bolts are also good for mounting the cap to the bed rails and provide tie downs in the bed.
Hope this gives you some ideas.