I've removed my post response - I'll post the question in its own thread. However, I raised the MC point in order to address the title of your thread "OoX in WW Timeline". I think answering the MC question might help confirm OoX with WW.

As to your specific point, I agree that Labrynna & Holodrum might be in the great sea, but since I don't really see any hints of a "de-flooding" in the games, I would go with the Deku Trees/Koroks being the prime motivators behind the geographical changes - At least that possibility was hinted at in WW.