Instead of silicone, look into butyl rubber. It does't harden or cure like silicone and is WAY easier to remove if you every want to touch areas up. Lasts way longer than silicone.
This person had a lot of good suggestions:
EcoTechne Roof Rack Installation (5th Gen)
If you look at greenland offroad's mount, it can be made water-tight with butyl rubber:
4Runner Aluminum Roof Rack System — GREENLANE OFF-ROAD
Same as RA motorsports (local to me in Canada) - this is the one I went with. I included a pic of their rack mount (3D printed plastic with a hard rubber + neoprene gasket)
03-09 4Runner Modular Roof Rack | Element By RA Motorsports
There are pictures of the mounts the rack mounts on to. So the key is go get one you can easily make water-resistant.
I also included a pic of the prinsu rack -that one suuuuuuuuuuuucks for trying to keep moisture out. You have to use a lot of something everywhere to keep water out.
I recently removed and sold my prinsu rack -the mounts sucked as they embedded into the paint and when you remove it, it removes paint which exposes bare metal. So I had to clean up all the mount points (very annoying given the small space you have to work with), etch prime, paint, and then clear coat. The prinsu mounts are round aluminum cylinders. The design of them cup water into the mount and concentrate pressure into the contact point on your roof.
