They may be talking about the 4x4 control box. On the passenger side the clicking noise is for things like actuating the 4 wheel drive. That doesn't go on all the time though, only while the 4x4 system tries to actuate or de-actuate.
Service tech is probably trying to dismiss it as normal since they don't always hear that one noise that bothers the vehicle owner. Just like a computer never does the troublesome issue when the IT tech is there to look into it.
I get a little ticking that I can't pinpoint myself since it is on the passenger side and not predictably repeatable and it has to be quiet inside the car while moving. I haven't mentioned it as it seems to depend on things like relative humidity etc.
Try these if you haven't already:
http://www.toyota-4runner.org/5th-gen-t4rs/158483-dash-click-rattle.html
https://www.google.com/url?q=http://www.toyota-4runner.org/attachments/5th-gen-t4rs/68468d1343138343-windshield-ticks-creaks-noises-36891417-t-sb-0141-10.pdf&sa=U&ved=0ahUKEwiHh6mEwdPNAhWI2R4KHf78DnMQFggHMAE&client=internal-uds-cse&usg=AFQjCNEHiyA3u-MbcYfJxxMZbQmLJB8A7w
Bummer on the TSB question too. I brought mine in for the complaint back in the 5K visit but it was too warm to repeat. They told me about bringing it in when cold too but I also opted to not waste my time since nothing was going to be done. I did ask about it again on the 15K visit so I am hoping that the documented mention will get the TSB validated. I will certainly post up here when I bring it in for the 25K and ask them about the TSB.