So is this why the changes in the RetroArch confg are never saved for the P2 bindings? Do I need to change that line in the Python script to remedy this? If so, where do I find it?

It doesn't matter overly now though - I've manually set the emulators for the few games that can get by on the other emulators (despite the save game location being different to proper "save" folders!). I've yet to decide whether to use this method or my manual config file.

I think if SNES 9x could be setup to only enable multitap when 3+ controllers are connected, it would be perfect. That and the save locations for the other emulators.

Other that that my setup is god to go. Thanks guys 🙂