I did recognize the Turtles from the live-action movies and the CGI movie (although those are supposed to be in the same universe, not two different ones).
The two were only quasi-related one another, in a similar manner of how Superman Returns was related to the Donner film. Besides, according to the rules of alternate universes presented in the special, considering one was CGI-Animation while the other was live action, that would make it enough for it to be another universe.
But I didn't spot the Turtles from the Next Mutation live-action TV series.
I think that's because the E&L (and most people in general) want to forget the whole thing ever happened.
And the toy universe, in which they lived in my basement and fought alongside the Ghostbusters.
That's the greatest universe of them all!