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