As of the r763 commit, inputs can be configured on a per-game basis. Prior to this, input settings have always been saved into the global section in Supermodel.ini, which means they would be the same for all ROM sets. In practice, this usually isn't a problem because many of the games have their own specific input devices anyway.
However, there have recently been some questions about inverted axes in some game variants. I don't know what the deal there is but with this new feature, it's irrelevant. You can now override your global mappings on a per-game basis. For example, if you want to invert the Y axis only in lostwsgo but not in lostwsga, you can now do that by specifying an inverted axis for the appropriate input there.
Running 'supermodel -config-inputs' behaves as before: input settings will be read from and written to the global section. But if instead you do 'supermodel romset.zip -config-inputs', input settings will be saved to only that ROM set's section in the INI file.