I didn't do it right because I sprung a leak at the first rain.
The offending installation: I removed the factory screw on the roof and drilled two new holes around it to mount the rack on the crown steel beam. I wanted bigger bolts than the #10 screws the factory was using.
The majority of the leaks appear to be coming from that center hole that I just left open. Bolted the aluminum right over the hole. A strip of butyl tape right over the aluminum mount plate in the crevice between the roof and the roof rack plate stopped the leak. This was the fastest fix seen below.
I also tried to squeeze a piece of butyl between the roof rack and the roof and rebolted on rack. Still had leaks through the bolt holes so I took off rack again and put scotch tape over the bolt holes. Looks like Butyl tape held over the center hole well enough but the bolt holes were leaking in this case. So the rack had to come off again.
The Butyl squeezed through the open hole under the roof rack.
I also tried a patch with a magnet and this worked as well. The advantage to the magnet is that it seems to provide enough force to hold the butyl tape but not enough force to push the butyl through the hole entirely.
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Temporary patches are working, no leaks into interior using these various methods above. This gives me time to plan a proper installation on the roof racks.
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So I have two different kinds of leaks happening. One is through the open hole I left in the roof by removing the factory screw. And, the other is through the bolt holes around the bolts. Each requires its own approach to sealing.
The bolt holes are easier, I think. The plan is butyl tape wrapped around the bolt placed into a countersink hole on the inside face of the aluminum mounting plate. The countersink should hold in the butyl and smush it around and into the bolt threads.
I'll make the counter sink on the drill press. I hear it is wise to be careful and avoid twisting the bolt and instead screw only the nut. This way I don't tear at the tape.
For the hole with no bolt through it I have to both patch and seal the hole. I am torn between eternabond tape and an epoxy to patch the hole. Then smush butyl over the top of that. Then mount roof rack and bolt down.
I am leaning towards an epoxy "core" pushed from the inside outward. Then put butyl tape down on the outside roof-side of the epoxy plug smushed between the aluminum mount plate and the roof. In order to build up a gutter away from the bolts I am going to use Dicor lap sealant, non-leveling. Little extra in the center to get the water away from the middle.