I haven't used Bootleg, and I can't help with the cutscene music, but I do know why the inn music doesn't work: It has never worked and will never work with FF7Music.
The problem is that the inn blacks the screen based on the length of the song playing, but when FF7Music is playing the music instead of the game itself, the game has no clue how long that song is, and immediately unblanks the screen and gets going again. The new version of Aali's driver doesn't have this problem, since it plays replacement songs itself instead of relying on an external program, but it doesn't work with Bootleg (at least, not currently).