My reasoning/evidence for why i personally think BoTW takes place after Twilight Princess… Possible spoilers…
The rock salt could come fromt the ancient sea mentioned in Skyward Sword in the Lanaryu province. In SS you can also obtain the “ancient sea chart”. So it doesnt have to refer to flooded Hyrule in Wind Waker.
Also the Koroks are an alternate sort of default appearance for the Kokiri. They looked like hylian children in OoT to make Link more comfortable, make him fit in…(they did such a good job). So it doesnt have to be the adult timeline for them to look like that.
The ruins of castle town are very similar to the look of castle town in Twilight Princess. A similar fountain and surrounding area. The maps of the two areas line up fairly well.
The ruins of Lon Lon Ranch… Its seriously exactly the same layout. The track is there, the gate…kind of sad really…
She mentions Skyward Sword (skyward bound), Ocarina of Time (adrift in time), and twilight princess(steeped in the glowing embers of twilight).
There is probably more evidence to confirm and deny this.. But its what i want to believe..until further notice.