So I just beat TOTK and after reading theories on the timelines I just wanted to offer my own.

1.First off I believe BOTW/TOTK take place in the same hyrule. Sonia was likely a descendant of Skyward Zelda, and her marriage to Rauru turned Hyrule from a small tribe to a Kingdom.

1. Second point is I believe there are 2 Ganondorfs...kinda. I believe the Ganon in TOTK is the og reincarnation of Demise, from his title to strength to appearance. After being sealed by Rauru, his gloom was at its weakest point.

2. Thirdly I believe Hyrule had peace for a few hundred years atleast as Sonias and Raurus descendants held the Kingdom together after their deaths. During this time the gloom slowly recovered before it became a weaker version of itself know as malice.

3. This malice made its way out of hyrule castle and reincarnated itself as Ganondorf once again but as a weaker version(though still powerful). BOTW states that Calamity Ganon was making itself a new body so this isn't a asspull. This new ganon is OOT Ganon.

4. We go through the motions after this as Ganon is sealed on all 3 timelines. Being killed finally in Zelda 1(fallen), Twillight(Child) and Wind Wakee(Adult)

5. Assuming BOTW is set so far in the future that all 3 timelines eventually happen, we can infer Ganon either kept reincarnating or kept being sealed over and over until eventually dying somehow.

6. In BOTW, more powerful and angry at a millennium of defeat, the Malice returns to its origin where its the strongest and becomes Calamity Ganon to just wreck stuff.

7. Then TOTK happens as you kill the OG Ganondorf, ending him and the gloom that kept its war on hyrule, even while its master was sealed.