Wisdom Tree eventually stated the whole thing was bunk and they paid for the license to use the Wolfenstein engine like everyone else, which id seconded while the game was unlicensed, it was only Nintendo who hadn't licensed the game. It seemed as though the game was basically one gigantic middle finger from John Carmack and John Romero to Nintendo's SNES-era censorship policies. So they outright gave the source code to Wisdom Tree and helped them get the Noah 3D mod running on the SNES (the SNES already had the engine operational, the game was basically just a mod, not much different from the many Doom mods you can still find today).
According to the rumor, id was angry about how Nintendo had censored the SNES port of Wolfenstein 3D. God Never Said That: For years, it was thought that the release of Super 3D Noah's Ark was a big Take That! to Nintendo.
It is possible to get the music working on emulators, but not with a standard cartridge on real hardware even then, it does not play properly as the music player code was left unfinished for whatever reason.