@mitu Thanks, appreciate the help.
I tried many times to autoconfigure the Nvidia controller (Manage packages -> Manage core packages -> emulationstation -> Configuration -> and run Clear/Reset Emulation Station input configuration) and recreating it, every time it created the same shorter name. Only using the Retroarch menu, the new longer file name was created. As soon as that file was created, I stopped seeing the "not configured overlay", and seeing "Nvidia controller on port 2" (or something along those lines). And the controller started working
I really think that there is something weird with the auto-creation of the Nvidia controller. It's possible that somehow Retroarch and the auto configuration use different APIs to get the device name? Or that the V1.03 controller is somehow behaving differently?
Anyway, hopefully anyone else with this problem will bump into this thread and get a possible workaround