I just spent a couple of hours messing with things, including messing with almost every CANBUS option for Toyota/Lexus I can find. Most of them work with the amplifier, so the CANBUS box does work like you said. The air conditioner does work, but no CANBUS option helps. I'll look into that next time with logs.
 
For reference, the air conditioner plugs into the CANBUS box separately, like this. It's very strange. 

I did not take this picture myself, it's from this installation video. https://www.youtube.com/watch?v=AfasaqmuN4k
I had no luck with the CD changer either, but I'll try the scan button next time and let you know if it does anything. I'll be sure to record a video, too.