Great idea! I know I'm responding to this late, but I was thinking how your suggestion would work. As we know K'un L'un appears on the Earthly Plane once every ten years. Why is that? I was thinking that the foundation of K'un L'un was built on a fault line that's connected to space time continuum via the crystals. It's possible that Master Khan used a spell of some sort that trigged ripples throughout time and altered different points of K'un L'uns history without the residents realizing it. Now I'm going with the theory that Master Khan isn't a God. He casted a spell to make himself a God to the people of K'un L'un but it had side effects that effected time and space and is still effecting it in his absence. That would be a great way to explain the inconsistencies without outright writing them off. As for the Ninja, I thought he was the one behind the recent attack in K'un L'un but it would be nice to see him return from his pocket dimension and cause havoc! He needs a new name.
As I mentioned above, all of that could be side effects of the space time continuum spell that makes it possible for K'un L'un to appear on Earth every ten years and a spell Master Khan casted years ago that further effected everything.