For obvious reasons I can't respond to everything you posted here but MF DOOM is a good example of an artist I'm a fan of who's music often disappears on Spotify because of sample clearance issues. My favorite song on Madvilliany "Raid" got removed for a year because the sample was discovered to be from some old South American show and was never cleared. The original artist happened upon the song on Spotify and got it removed until they worked it out. I know Sonic Rush's soundtrack was sample HEAVY so to work out who needs to be cleared with what would probably be too much for SEGA to want to figure out just for a spotify release that won't even make much money. Might also be holding back any type of rerelease or remake too. It is what it is.