My main concern is how you can think MM is merely loosely affiliated with OOT. Me being a believer of the split timeline, in the timeline where Link and Zelda are children and warn the king of Ganondorf's intentions, Navi leaves Link and he sets out to find her. This leads directly into the...
I'm not sure that Zelda could exist without a coherently established timeline, it would just seem a bit too much of a stretch.
Granted it makes sense, but I just don't find it likely.