I think Nintendo VGM -> a Tool album is a bad comparison. First, a band obviously makes its music widely available, but might not want to be on streaming services that return thousandths of a penny on the dollar. Nintendo offers no legal way to enjoy the music without directly playing through the game.
Which gets to the second point: the music isn't the main product for a games company, it's one side aspect. It would be more like a band refusing to show its music video unless you happened to catch it on MTV thirty years ago. You chose not to monetize it, and it only makes you more widespread and popular, so why bother going after fans?
It only makes sense to attempt if you're used to locked-down proprietary systems (and not the infinite whack-a-mole of the internet) or you similarly misunderstand and think you're in the Tool business.