The "WKTJA4, WKTPA4 - CONTRA REBIRTH" thing actually has no effect. Every line that starts with a # is a comment, meaning that it's completely ignored by Dolphin. As long as the first three characters of the game ID match an a three-character INI name, that INI is used.
I do recommend putting cheats in six-character INIs instead of three-character INIs, though. Cheats are usually only compatible with one version of a game, so using a six-character INI ensures that you won't accidentally apply the code to incompatible versions of the game.
I do recommend putting cheats in six-character INIs instead of three-character INIs, though. Cheats are usually only compatible with one version of a game, so using a six-character INI ensures that you won't accidentally apply the code to incompatible versions of the game.