Just copy these files in the ZIP into the same folder that you have the games in the archive. Make sure they have the same exact name ( minus the extension ) as your game. This will allow the game to work. Basically what I did is I loaded the games in Stella on the PC and went into the settings and forced the controller type and saved the settings ( .pro ) file. Stella for retroarch will read these files in if they have the same name as the game.
I had opened an issue for this somewhere.. but I forget where. I'm hoping to look into it once I'm done with Atari800 and Hatari for retroarch. Stella is next on my list of things to look at. Nothing fancy.. probably just a few minor touchups. ( Unlike Atari800 and Hatari ).
Here it is.. love the tag they gave it.. (rolls eyes). core bugs - not retroarch bugsinvalid: won't fix
They could "fix it" by connecting some of the stella functionality back to the retroarch core options. So more accurately it's an issue exacerbated by the retroarch interfae
https://github.com/libretro/RetroArch/issues/12467#issuecomment-1405660334
RetroStella.zip