One way that did make a difference was in earning multiple instances of Shrykull, which mattered with the changed side-scrolling format and some of the adapted puzzles. The addition of "All o' ya!" that this necessitated also required the subtle adaptation of some of the puzzles, particularly in the secret areas with repetitive elements, to maintain their strategy.
I suspect the primary reason was not to raise difficulty (the guys at JAW aren't stupid and knew that wouldn't happen, they played the damn thing), but rather to give Rupture Farms a workforce large enough to actually run the Biggest Meat-Processing Plant on Oddworld.
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