The major issue I have is that RetroArch input mapping works great, but it doesn't work well with Dolphin or OpenBor or Ports or ScummVm which is the bulk of my gaming. So, that's why I have a hodgepodge of RetroArch, gamecontrollerdb.txt and other stuff going on here.
Not sure why you think RetroArch's configuration is relevant for the standalone emulators - they're entirely separate. Or maybe I'm mistaken ?
I've managed to get joy2key_sdl going. I have 2 8Bit Do Pro2 controllers. Interestingly, when they are by Bluetooth they are called "8BitDo Pro 2" and when plugged in by USB they're called "8BitDo 8BitDo Pro 2".
Yes, that's not un-common for gamepads, having different names and/or input mappings depending on the connection type. 8BitDo are even more eggregious in their behavior since they have also different connection modes (Xbox/PC vs. Switch vs. Android vs. etc.)
When plugged in I get "configured device" despite having a separate "8BitDo 8BitDo Pro 2" config file in /retroarchjoypayds
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and I have this config I sourced from 8BitDo which might be a better bet?
How can I get the USB and Bluetooth connected controller to behave similarly?
Just configure the controller separately for USB and Bluetooth. The input codes may not be identical between the connection types and you can't rely on a firmware update to now change them.
Also, the mapping is rather strange, despite my mapping in the 8Bit Do Pro2 config, it is coming out wonky and despite it working ok in Retroarch and some other configs. Why the pageup and pagedown stuff?
Not sure what you mean here.