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I think the difference is in the episode they debut in, Shredder/Krang decide to mutate them as a second set of henchmen after Bebop/Rocksteady. The difference is Groundchuck and Dirtbag betray Shredder almost immediately and decide not to listen to him, so that plan backfires.
Much like Rahzar/Tokka in the movies working for Shredder, Groundchuck and Dirtbag were conceived as a second mutant henchmen pair the same way...they just didn't pan out like that.
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