While having the TMNT visit Usagi's world was fun in the comics, and it's understandable how it doesn't exactly fit into the UY regular continuity--happily the opposite is true for the TMNT side.
Having establised super heroes, mystic elements, aliens from space, and all the other stuff--it's perfectly natural that Usagi could have made contact with the TMNT.
Some issues of Tales of the TMNT, and even some of the old Mirage issues, went into some alternate kinds of stories. Michael Zulli's Soul's Trilogy was not at all the regular continuity, but an alternate version "what if" kind of thing. I don't know if Peter considers the crossover stuff with Usagi to be in or out of "regular TMNT continuity." As I wrote, I prefer to think of it as "in continuity."
I agree with some other comments on this thread, that my perecption was the TMNT that were summoned into Usagi's world were the TMNT--but as I seem to recall Stan admitted at a convention some years ago, something about not always being able to remember which personality of Turtle went with which name--other than Leo because of the swords made it easy to remember him?
At any rate, I have enjoyed the fact there were able to be a few crossovers, and moreover, that Usagi was able to be on the new TMNT cartoon. I am looking forward to seeing the new pin-up, too.