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I'm a Transformers fan and contributor at TFWiki.net, so I tend to see things from the TFWiki point of view: "everything is canon, but not everything is in the same continuity."
The Super Turtles OVAs are canon with the Japanese version of the Old Toon, which only ran for 101 episodes.
So I just see the US and Japanese versions of the show splintering off after 101 episodes into two separate continuities. The US goes in the direction of the rest of the series as we know it, into Red Sky and all that, while Japan went with the Super Turtle OVAs.
I've always rationalized it as such and been content.
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