A little update, I removed all configs related to Mednafen PSX and now I can save specific game options, sorry for the confusion.
Also, it seems that TR III, in its latest revision works with DS, don’t ask me why.
The “Create Game Options” let me save some settings, but it just saves my remaps when I save game overrides, so there are varied parts of configurations in the latest updates that will probably let some people confused in the near future, I think.
Remaps are reloaded in some other cores I tested, but not in Mednafen PSX, but Radius explained that earlier, the only confusion here is why other cores are reloading remaps if it’s getting obsolete and merged in other configurations, like overrides.
I tested Tomb Raider II, it seems to only works with the original Joypad, no other gamepad, like Dual Analog or Dual Shock works, the game pauses immediately if you switch any other gamepads, that can be solved with the auto ON/OFF for the analog, but I still don’t trust it will work for all games, letting some that are compatible with analog, with analogs turned off, so I could only remap the joypad using game overrides.
In Short:
Dual Shock Analog Button Toggle (ON) will probably make all your games recognize your inputs, but I tested Driver 2 and it turns analog off, even the game being compatible with Dual Shock and probably Dual Analog, this happens with other games as well.
Saving Remaps only creates a blank file, in Tomb Raider II and earlier PS1 games only works with Analog OFF or with the original joypad, to save the analog we’ll need to use Save Game Overrides, now the correct remap will be loaded.
While some games works perfectly with Wide Screen Hack (ON), even using 16:9 stretched video, some will not and this option will only be saved for that game using Game Options saving, not overrides, that was what Radius was explaining earlier, I think, somethings are related to the core itself and somethings to the frontend, right?
I’m fine with it now, the confusion was created here because somethings were changing and will probably change in the near future, everything is working perfectly fine now.