The Toyota installation instructions for my 3rd Gen roof rack called out 3M Ultrapro Autobody Sealant Part# 08302

Amazon.com: 3M Ultrapro Autobody Sealant, 08302, Clear, 5 oz Tube : Everything Else

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I used RTV silicone, and it seems to be doing the trick.

Make informed choices when deciding what to use when sealing roof rack mounts.

Destroyed Factory Roof Mounting Locations

This is a bad reference though. The OP later explained how the damage in the initial post happened.

He never once inspected the seals after putting the rack up. This happened more than 5 years after installing the rack. He linexed the roof up to the seams of the rack. He kept it outside in Hawaii for 5+ years, and had annual periods of up to 6 months at a time where it was never moved.

I'm installing my full length victory 4x4 rack today and plan on using the black RTV as they recommend. My 4runner stays garaged in the PNW and serves as my daily driver to and from the garage at work when not out on weekend trips.

For those that fear water intrusion despite following the installation guidelines, maybe you should reconsider the necessity of an after market rack.

I had a leak after the dealer replaced my rack at the port. I took it back to the dealer shortly after discovering the water intrusion and was told they didn't have a "diagnostic technician" on duty (I was told this AFTER making an appointment for a leaking roof rack). I found it much easier on my time and frustration level to pull/wrap all of the bolts in teflon tape and retorque.

Haven't seen/felt a leak afterwards.

I'm not sure why you think it's a bad reference...

If you only read the first post, then I could see your point.

It was an example of what could happen, which is why I posted it. Obviously you want to read the full thread, if you're changing roof racks.

If I were to do it again I would probably go with butyl tape, and make sure the bolts have some kind of metal washer not the OEM bolts. My rack leaked driver side, pulled out wet seatbelt one morning...oh crap...
Despite careful silicone application I think it was a shrinkage issue, pretty sure b/c I was very methodical at install.
That particular roof rack reuses OEM bolts though and everything sit exposed to UV slowly breaking down, would only be a matter of time without the cover caps that OEM rack has. I took it all off and went back to OEM rack to get that piece of mind, I guess those Toyota engineers were onto something after all

I used globs of silicone RVT years ago and haven't had a problem. Obviously, there are less messy alternatives now that weren't available 5 years ago. Too lazy to redo it.

You apparently failed to read what I wrote, or else you would have seen that I referenced OP's reply and explanation for how the water damage happened which was on the third page of the thread.

I guess the fact that you quoted me, and called it a bad reference, made me assume you were referring to me...

I applied butyl tape when I installed my Prinsu last year. No issues so far.