In my recollection, most games that actually support reconfiguring the controls still support that; the Pandora (and Pyra) specific joystick layout (which it like that because it really speeds up navigating the desktop and entering text, and they're just extra buttons in that context) if the default but you should still be able to reconfigure it. Only games which haven't provided that feature as a menu item don't often get one added by the porter, but you might still be able to do it via a config file in your appdata folder, but the details on how to do that are often various and badly documented, but that's the fault of the original author, or perhaps the porter for not linking to that documentation properly. It's usually not hard to navigate from a port to it's original github or whatever source, where the original documentation lives. But yeah, you'd have to do that with everything you want to play every time you want to use the joystick most likely.
