Looks like the Link is dead theory is a lot more debated than I thought. I never really liked it myself. The Navi is dead theory makes more sense, but just feels off. One of the main pieces of evidence, that I've heard, is that faeries vanish when used. I've always imagined that they teleport. This would suggest that they could vanish any time they like, meaning that they stay in the bottle by choice, and explains how they so easily get out of the bottle as link starts to die. But, that's just off the top of my head.
Personally, chevys head canons about botw link being oot link and tetra/zelda being a case of multiple personality disorder irk me for obvious reasons
What? And, what!?
How does the first one even work?
Tetra/Zelda does not fit the requirements for having a multiple personality disorder.
Anyways, as for the original question, I've seen BOTW's timeline placement hotly debated on this sub. Many agree it fits best in the Adult Timeline, but it's always a cause for a heated discussion.
I found that out the hard way. I'm personally for the downfall timeline placement, though I've recently theorized that if the game takes place in all three, then all timelines tend towards the downfall state.
But what is a theory, other than speculation with evidence to back it up?
These are the questions I think we need to ask. The more we analyze how we theorize, the better we will become at theorizing, and the better we will be at understanding where our ideas come from.
For me, the difference between headcannon and theory comes down to two points; evidence, and crystallization. A (good) theory is based on evidence, and is flexible. Headcannon doesn't need evidence, and is usually inflexible.