They did mention more than once that this is "before" they became Ninjas and their adventures before "we know them" from other versions. They haven't emphasized it as much as the magical aspect but they've definitely mentioned it.
I mean I agree with your points about how it'll be similar to say Smallville or Gotham where established things in universe will happen before they're "official" and the magical aspect will also be odd but hey who knows how they'll handle it. I do think a "batman begins" of TMNT could be a cool idea but also mixing it with a "magical underground NY" leaves you like "what?"
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