I'm guessing that even if OP's T4R were still under warranty, Toyota would not honor a claim for frame rust. As I understand it, their rust limited warranty is for painted surfaces, not underbody components.
I also hate the rust on the chassis of my 4Runner, but believe it will probably take another class-action lawsuit against Toyota to get any satisfaction. And said lawsuit would probably only be successful if it can be proved the frames are severely damaged by said rust causing a safety issue. On my '08, the rust appears to be cosmetic so far.