The game uses not only sub-segments, but it looks like it uses channel muting as well... and even speed variations! Using my official music modifier, I was able to get every last sub-segment, and determine variations, if any.

This is a massive cleanup effort: I have acquired every single variation possible. Plus, that means I redid the numbering. First... the original track names and their new assignments (directionals are reversed... it's right to left)... as well as any markings either for a redump, new track, or if the original dump is good:

Egypt 1 <- Egypt 1 (original dump is good)
Egypt 2-1 <- (new track)
Egypt 2-2 <- (new track)
Egypt 2-3 <- (new track)
Egypt 2-4 <- (new track)
Egypt 3-1 <- Egypt 2 (redumped)
Egypt 3-2 <- (new track)
Egypt 3-3 <- (new track)
Egypt 3-4 <- (new track)
Egypt 4-1 <- (new track)
Egypt 4-2 <- Egypt 6 (redumped)
Egypt 4-3 <- Egypt 5 (redumped)
Egypt 4-4 <- (new track)
Egypt 5-1 <- Egypt 4 (redumped)
Egypt 5-2 <- (new track)
Egypt 5-3 <- (new track)
Egypt 6 <- Egypt 9 (redumped)
Egypt 7 <- Egypt 3 (redumped)
Egypt 8 <- Egypt 8 (redumped ~ it was originally sped up)
Egypt 9 <- Egypt 7 (redumped)
Space 1-1 <- Space 1 (redumped)
Space 1-2 <- Space 7 (original dump is good)
Space 1-3 <- (new track)
Space 1-4 <- (new track)
Space 2-1 <- (new track)
Space 2-2 <- (new track)
Space 2-3 <- Space 3 (original dump is good)
Space 2-4 <- Space 4 (redumped)
Space 3-1 <- Space 2 (original dump is good)
Space 3-2 <- (new track)
Space 3-3 <- (new track)
Space 3-4 <- (new track)
Space 4-1 <- Space 6 (original dump is good)
Space 4-2 <- Space 5 (original dump is good)
Space 4-3 <- (new track)
Music 1-1 <- Music 1 (redumped)
Music 1-2 <- (new track)
Music 1-3 <- (new track)
Music 1-4 <- Music 9 (redumped)
Music 2-1 <- (new track)
Music 2-2 <- Music 10 (redumped)
Music 2-3 <- Music 4 (redumped ~ either it was slightly slowed down or it tripped...)
Music 2-4 <- Music 5 (redumped)
Music 3-1 <- Music 2 (redumped)
Music 3-2 <- (new track)
Music 3-3 <- (new track)
Music 3-4 <- (new track)
Music 4-1 <- (new track)
Music 4-2 <- (new track)
Music 4-3 <- (new track)
Music 4-4 <- (new track)
Music 4-5 <- Music 3 (original dump is good)
Music 5-1 <- (new track)
Music 5-2 <- Music 11 (redumped)
Music 5-3 <- (new track)
Music 5-4 <- Music 6 (redumped)
Music 5-5 <- (new track)
Music 6-1 <- (new track)
Music 6-2 <- (new track)
Music 6-3 <- Music 8 (original dump is good)
Music 6-4 <- Music 12 (original dump is good)
Music 6-5 <- (new track)
Sky 1 <- Sky 1 (original dump is good)
Sky 2-1 <- (new track)
Sky 2-2 <- (new track)
Sky 2-3 <- (new track)
Sky 2-4 <- Sky 6 (redumped)
Sky 3-1 <- Sky 2 (redumped ~ it was originally sped up)
Sky 3-2 <- (new track)
Sky 3-3 <- (new track)
Sky 3-4 <- (new track)
Sky 4-1 <- Sky 4 (redumped)
Sky 4-2 <- (new track)
Sky 4-3 <- (new track)
Sky 4-4 <- Sky 3 (redumped ~ it was originally sped up)
Sky 5-1 <- Sky 5 (redumped)
Sky 5-2 <- (new track)
Medieval 1 <- Medieval 1 (original dump is good)
Medieval 2-1 <- Medieval 6 (original dump is good)
Medieval 2-2 <- (new track)
Medieval 2-3 <- (new track)
Medieval 2-4 <- Medieval 4 (original dump is good)
Medieval 3-1 <- Medieval 3 (redumped)
Medieval 3-2 <- Medieval 8 (redumped)
Medieval 3-3 <- Medieval 7 (original dump is good)
Medieval 4-1 <- Medieval 9 (original dump is good)
Medieval 4-2 <- (new track)
Medieval 4-3 <- (new track)
Medieval 5-1 <- Medieval 5 (original dump is good)
Medieval 5-2 <- Medieval 11 (redumped)
Medieval 5-3 <- Medieval 10 (original dump is good)
Medieval 5-4 <- (new track)
Medieval 6 <- Medieval 2 (redumped)

Additional redumps:
Hub
Boss 1
Boss 2
Boss 3
Armadillo Mini Game
Bubsy Dies
Victory and Game Over

New Tracks:
Armadillo Mini Game (Variation)
Frog Catapult Mini Game (Variation)
Fly Up
Fly Down
Score!
Underwater Mini Game (Variation)

The official tally:
56 new tracks
33 redumps