Did no one honestly read what I posted? I explained the geography. <_<
Flat areas cannot create islands. I don't know why that is commonly discussed?
I'll be the first to address this, as your two comments thus far have set off a time bomb in my conscience. If you actually read the first post, you'd have realized that the locations for all my theories did match up, and I did in fact factor elevation. Still, I cannot imagine the flood being overly devastating since many areas low to the ground have been proven to be islands in Wind Waker (such as te Kokiri Forest and Forest Haven). Plus, while I compared general location, you tended to stray too close to reality. Zelda is not reality. Also, I'd like to take a look at a previous post of yours.
So i've turned the two maps in all sorts of directions in relation to each other, rather than having them both upright like how they're displayed, and still they don't geographically add up. I'm putting populous disputes and my hatred for the acceptance of Zora>Rito bit aside and seriously trying to tie things together geographically. The best I can think of is that there is much more landscape than thought of than is made up of nothing but mountains, because there are only a few high elevations in hyrule. It says that the godesses flooded the place, not changed the landscape contours, so everything is still going to be where it was in the first place.
Anyways here are a few of my takes on this.
The tower of the gods is directly above Hyrule castle. That part is set in stone. The tower itself isn't an island so it wasn't ever a mountain. I almost feel more like Dragoon roost is more the Gerudo fortress. Dragon roost is tall like the gerudo fortress, not widened out like death mountain. Which would make more sense that bomb island is the top of death mountain. Geographically it's in the right amount of distance, and the fact that it is the "bomb" island only gives it more relation to death mountain.
This in turn makes the relation between the forest haven and the lost woods even clearer. Again it is in adequate relation to death mountain and the sunken hyrule's location. Which in turn keeps the Deku tree in the same location. I'm sure the Deku tree could have been replanted in the same relative location, or just been revived.
The rest of the map is covered in clouds and could easily be a ton of more mountains. I'm just clearing the geographical understanding up.
The Gerudo Fortress is Dragon Roost Island? Ilogical. You're the one that talks of location, yet the two are nowhere near each other. And Bomb Island is Death Montian? Bomb Island isn't near as large enough or near the spot on the map. There are not many similarities, including that it doesn't sport a dungeon inside. Also, I'm sure the Deku tree is in the exact same location as before.
I agree with all of your connections, except Lake Hylia = Outset island. One important factor when taking this into account is that Jabun, who is likely to be or at least be a descendant of Jabu-Jabu, feld to Outset island because of Ganondorf. Jabun's original location was Greatfish Isle. However, on the WW and OoT maps, they are on opposite sides. Also, there isn't really a match to Zora's Domain. However, one could say that Zora's Domain is a part of Dragon Roost Island. After all, the Rito evolved from the Zoras, so perhaps they evolved because their habitat was changing as well.
Another interesting fact is that the Tower of the Gods is directly above Hyrule Castle in WW. What structure do we know from OoT that was tall like that? Ganon's Tower. Perhaps in between OoT and WW people rebuilt Hyrule Castle with the long segment from Ganon's Tower with another purpose - to worship the Gods. Then, there is the question about Lon-Lon Ranch. There are two options for this: Tingle Island and Windfall Island. I think it would be Windfall, as Tingle Island is just way too small. Perhaps its community could have merged with the one from Castle Town.
I understand the first part, PT. And I congratulate you for pointing it out. See, Lake Hylia's location in the future seems to be the most shrouded in mystery as there is not much to investigate. I have taken what you said into account, and actually, thiswas one of the things I thought would come up - Jabun.
The second part, I'm afraid, is notas impressive. As many others pointed out, Ganon's Tower from Ocarina of Time is likely Ganon's Tower in Wind Waker. The Tower of the Gods was likely created after the drowning of Hyrule because the three statues of the goddesses (on the islands) did not exist in OoT either. It's safe to say that the whole Tower of the Gods deal was created as a way of testing the chosen hero, but only after Ocarina of Time did it come to be.
So for the most part, I agree strongly with Locke and Djinn.
) but think about this, hyrule castle is located underneath the tower of the gods.. so if hyrule castle is located underneath the tower of the gods so is the castle town market. It is only logical to think that. But this is only what I think.. I could explain more but I am just giving you a thought. 
