Though I can see the rational for why just about any or none of the Timelines works for BotW. I still feel strongly that it would take place in the Adult/WW Timeline.
Let's look at some of the reasons OP states:
Is this correct? So lets look at this from certain Perspectives:
Then of course you have the events of TWW itself.
Which leaves a bare minimum of 3 Times that Ganon has attacked Hyrule.
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Now lets look at Hyrule itself, now of course in the Adult timeline, Link and Zelda leave old Hyrule and find new Hyrule while what remains of old Hyrule still stayed preserved under the sea. The item Rock Salt indicates that Hyrule was covered in an Ancient Ocean, and of course 10,000 years ago already being in the future of any of the timeline, then TWW's ocean would be pretty ancient.
The Islands of Windwaker for the most part were just the tips of Mountains however, so without the Ocean, the land mass would have a lot of mountains. Which BotW's hyrule has. Easter egg or not, If you look at the raised points of the Hebra Mountains with the Island where the Forsaken Fortress is in TWW, the overlay is fairly identical.
Another thing to note is the Locations the Deku Forest. Sure it's relocated, but the Map kinda indicates why as well. You had the Koroks in TWW try to rebuild the Flora in the land, which explains it's movement, but if you look at the map once again.
Theres a Spot by Deya Lake in the South Eastern part of Hyrule that also matches up with South Eastern Part of TWW Hyrule:
Yes, I'm implying that could be the remains of the Great Deku Tree of TWW.
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The Zora/Rito connection.
Look, I get it, how can their be Zora's if Rito's evolved from them?
I mean how can Wolves still exist if Dogs evolved from them?
Hyrule IS NOT the World. Multiple Zelda games have made that known. It's likely the Largest/Most influential land, but it's not the end all be all. Zora's exist in the Kingdom's of Labrynna and Holodrum in the Oracle Games. Either way, proof that Zora's aren't just from Hyrule. So there's Multiple scenarios that can be inferred from this:
Just like when Hyrule Flooded and Zora's were given the ability to become Bird like to Survive, than the same could be true when it became unflooded, They could've been given the choice to remain Rito or Revert to newer Zora's and you might've had a split, some choosing to remain and some choosing the change back.
OR
The Rito migrated to a new plain once Gorons reclaimed Death Mountain for themselves and with the repopulation of Old Hyrule, Zora's from other regions, would've settled.
OR
It's a combination of both. Reason why, is that the Zora of BotW are the most genetically diverse of the Zora's represented. Most Zora's up to this point have shared a new universal look, but now we have them in Multiple hues. Genetic diversity in the wake of changing landmasses happens in the natural world, why would we thing otherwise for Zora?
This also falls in with the Lynel camp. Just because it exists in one timeline doesn't mean it cant exist in another. If 2 of the WW Races can sapossedly exist in the Downfall timeline, than whose to say the same isn't true with Lynels?
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OP also stated this:
I see that and raise you a
So this can be taken multiple ways. The Master Sword being immobile has been disproven time and time and time and time again, SOMETHING'S gotta be relocating this from one pedestal to another in the past of each game.
If Zelda's Legends prove anything is that nothing is "Forever". The state of Ganon in BotW is that of a man continuously trying to change fate and undo his own mortality. He could've left or ascended past his old body, or some dumbass pulled the Sword from his Stoned body to allow for such a thing. Everything is theory but this guy ALWAYS finds a way back, whether by his own means or by his followers.
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Anyway, that's all I'm willing to type up at the moment. I've actually been itching to debate this timeline for months.