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I bet that in the original script for the first one, where they used the mutagen on the Foot to create super-soldier mutants, that idea was pitched with the idea of using a similar method to create Bebop and Rocksteady in the sequel.
So, it could be a remnant of a discarded earlier idea, basically. It might be tough to explain in this one, but possibly easier if they had kept the original plot for the first one intact.
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