Show me a link, I may be wrong.
http://www.toyotatundraforum.com/pdf/A750E.pdf
CH-2, section 4 says flex lock-up in 3rd gear as well. I imagine it the flex lock-up was added to 3rd gear sometime after the doc you linked.
Talking to the quality engineer at my plant, he was saying that flex lock-up is available in 2, 3, 4, 5, and 6th gear of our transmission*. I'm a production engineer, so I don't have that understanding of the assembly testers, but it sounds like Toyota is pretty aggressive with the flex lock-up these days. I might have to check the TIS at work tomorrow to confirm for the 4Runner.
Neat fact about the Aisin 5ATs in our 4Runners: AWNC builds the A750 in North Carolina and exports some of them to Japan. Some of those exported ATs end up in 4Runners. Despite having japan built 4Runners, some of us might have US built ATs.
* My transmission is a transverse mounted FWD/AWD AT and is a more recent design than the A750.
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