I recently got the JP version working on my Wii VC to start speedrunning this game, but the aspect ratio for some reason is at 16:9, and the normal version of the game should be 4:3. Is this allowed?

The resolution of the game is all dependent on your wii settings. The game is meant to be played in 4:3, so make sure your Wii and TV is set to that aspect ratio (the aspect ratio does not affect the speeds in anyway, so you can play on whichever resolution you like but... 4:3 is better.)

Thank you, I realized the problem was I forgot to change my capture card resolution, so OBS was outputting 1080p resolution regardless of what I set the Wii console settings as.