TLDR; ctrlr input settings doublely won't work for Space Wars, so you need to use the game's specific cfg file as you found out.
- ctrlr settings change the "Input (general)" inputs. The "Input (general)" inputs are only used if a game's inputs aren't modified in the source code or in the game's/parent's/source .cfg files. Games like Space Wars modify those inputs you pointed out in the source code (see next on why this game does). There is a hack to get around this limit if the input type is a normal type (example: Toobin), but it won't work in Space Wars because:
- Space Wars uses the input type "Other" for the buttons. "Input (general)" has only one "Other" input, so even if you could get around limit 1) above, All the buttons would be set to the same input button. The game can have more than one "Other" because of the "mask" and "defvalue" qualifiers, things that only are valid in cfg files, and are ignored in ctrlr files.
I can go into the work around for games that use normal player/buttons or player/joys, if you want me too. The thing is the work around is more work than just normal remapping is. And doesn't work for Space Wars anyway (at least not without editing the source and recompiling).