It's a cool idea. I've thought this myself before.
But then I -- and probably 80-90% of people -- do almost all of my music listening these days via Spotify (or similar) and YouTube. I no longer have vast collections of MP3s immediately to hand, and I'm not sure I'd be bothered to fiddle around moving files in and out of folders, when I can just play the songs I want in a tab in the background. I definitely agree it would be better if it was all done inside the ship menus, and within the game's soundstage, but that's becoming less and less of an easy, seamless thing to manage these days.
I mean, an MP3 option would be better than nothing, but I'm not sure they'd do it, because I'm not sure how widely it would be used, compared to just five or ten years ago when it was commonplace to have your entire music collection on a hard drive.
Maybe if Spotify or Deezer or someone released an API that let commercial games hook into their libraries, we'd see more games using this kind of feature, perhaps alongside an MP3 playlist option.