Okay, you do have a point, but it's a pointless point, because even if the Deku Tree's Success was in fact taken into account in RPTRR, it hasn't been shown in any main series Zelda game. Also, while it might in fact be the islands of the Great Sea coming together and the water level dropping, many years after TWW...it could also be many years prior to TWW, in a newly flooded world. This seems even more likely, because people remember landmarks like Death Mountain and Lon Lon Ranch, while in TWW nearly everything about Hyrule has been forgotten. Or, a third possibility...RPTRR isn't canon at all, in which case it doesn't connect to the main series Zelda games in any way, so any "evidence" you draw from PRTRR means nothing.