I'm getting quite confused with this theory, but this is what I think:

In my opinion, I doubt that Majora's Mask and the Fused Shadows have any sort of historical connections between the two. It is amazing at the fact that they have so many similarites and similar historical events that happened.

But I doubt that the Twilis had anything to do with Majora's Mask. It might have well been another tribe that died out hundreds of years ago where they mastered hexes and curses to a point that it might have wiped them all out.

All I can say is that it is a terrific coincidence.