Too many to mention.
Why did Pixel pick .org rather than, say, .mid or .mp3 or .ogg? :-/
I've worked with OrgMaker before (it's actually a nice DAW for making music) and I'm guessing it has to do with 1) the readability of the notes through CS and 2) there are a set number of instruments.
It'll be easier on the game if all the instruments are already defined and you just pick and choose the timbres you want. Then note data will function similarly to .mid files, where it's just instructions on how to play the song.
Mp3 is too heavy of a file format and not very effective when it comes to file size. If CS had .mp3 instead of .org, the music would probably be at least 10x larger than the game's file size.