I had difficulty programming 3 separate iDrives by Wayne Dalton, and all of the normal instructions in the Lexus manual and WayneDalton manuals didn't fully work. Here is what I had to do. Maybe for those who have tried everything else, this may work.
Use the large center button on the iDrive remote to do the programming. The other 2 buttons won't work. The center button has to be programmed to the iDrive that you want to use with the HomeLink button. Thus, you will need 3 separate remotes to program 3 buttons.
Erase the Homelink on your visor according to the Lexus manual.
Press the desired HomeLink button and the center iDrive remote simultaneously until the flashing completely stops. This took a full minute for me.
Press the Learn button on the iDrive, then press the HomeLink button for 2 seconds, release, and repeat until the iDrive beeps.
Test.
If you want to program a second or third button on the HomeLink, use a different remote, and follow the intructions above.
Hope that helps someone avoid the pain that I went through!