You are indeed misunderstanding. The soundtrack will be included with the game, it just cannot be IN the game. And who said anything about it being of lesser quality? The renowned Super Metroid hacker Digital Mantra did the same thing with his re-release of the SM hack Eris, and people loved the soundtrack. This will count as the games soundtrack, and we can specify in the track info where and when the music is meant to be played. The only reason this music would not be within the game itself is because the only way to make custom music within Super Metroid would require a person interested to learn complex ASM code, so instead it would be given alongside the game to be heard.
EDIT: In reply to you, G-Mixer, the point is that this is how the game is meant to be heard, but cannot be, because of the way the music of Super Metroid was coded. So to give people full enjoyment of the game, a soundtrack would be provided alongside it.