As a final post for the benefit of others, I did not know if AHK could "send" joystick buttons in the script. So, in Retroarch I set up two "enable hotkeys", one being the select button on the joystick, the other being "q" which appeared to be unused. You can set multiple binds for that function.
I then added the q button as a send key down (first) and up (last) in the pause menu scripts for the various functions that required button presses (reset, save, load), and it worked! I could also use the select key on the gamepad to rewind (with select+L), as well as save state (select + R), and the pause menu functions worked. Just be careful...I inadvertently in the load script had send q down twice, instead of down and then up, and that caused the joypad not to work when I loaded a save state as I assume Retroarch disabled all the buttons assuming the hotkey was still pressed.
I use Retroarch's auto save states so that it increments the slot on its own.
Hopefully this is helpful to others.