Protip: The base is irrelevant, and the rom filename is irrelevant. All that matters is that you have a proper config.ini file for your rom that matches your proper filename. So for example you have MarioKart64.z64 in the rom folder? Your config.ini needs to be renamed to MarioKart64.z64.ini and placed in the config folder. ALL the other ini files in the config folder can be safely deleted since they are for other games.
I injected Donkey Kong 64 into Super Mario 64 with its official config.ini just to see if the bases were different, and if the bases weren't uniform, this absolutely would have crashed. It's interesting how many games Nintendo has made ini files for that they won't be releasing, for me Mario Kart 64 and Mario Party 2 were the ones I ended up wanting.
I'm definitely interested in setting up some kind of debugger setup. If we could try running unsupported roms, figuring out where they crash and building custom config.ini files off that, it's possible we could support more roms than currently available. (Or not I'm just spitballing ideas right after waking up)
Another tip: If you started messing with files in the meta folder, you could change the game name and icon and etc so it actually shows as your game in loadiine. Unnecessary for the most part, but I was glad to have all my games show up as the proper title
I also gave my injections custom TitleIDs that other games wouldn't be using so there wouldn't be any conflicts down the line (Like INJ101, INJ201, etc)
Anyways sorry for the long ramble post, hopefully there's something helpful in there