Hi @mitu ,
I'm returning to advise you of my good fortune and to help any others who may have been in the same situation as me.
I had been using my Xarcade tank stick controller in "Mode 1" with the Xarcade2Jstick driver which meant that Retropie was recognising it as a keyboard (iPac-type encoder).
I have now switched the controller to "Mode 4" and omitted the driver which means that Retropie recognises the controller as two separate XBox 360 controllers.
I can now configure each side of the controller with identical mappings and any game/platform I wish to use the right side instead of the left side of the controller, I simply change the Port 1 binds for in Retroarch.
When I do this, Hotkey+Start (even on the righthand side) performs correctly and exits the game.
Thank you once again for your help mitu.