Juicie, I believe that you are wrong on this one, though you are not wrong often. The Forest Temples from the two games are far too dissimilar to be the same structure. The structure and layout are far too different for them to be the same.
I present Exhibit A: The structure of the temples:
Exterior of
Ocarina of Time Forest Temple.
One room of
Twilight Princess Forest Temple.
Notice, first of all, that the overall structure of the
Ocarina of Time Forest Temple shows that it is clearly man-made, and constructed from stone. The wall is decorated and the structures on the edge of the roof are ornate. There is an obvious wood door. Inside, all the walls are stone and many of the areas do seem like chambers that have not even been overgrown by the forest greatly, though some of the areas do seem quite forested.
Compare that to the image of the
Twilight Princess Forest Temple. The structure seems to be mostly composed not of stone, but actually of the combined trunks of many trees. If you look closely, it does seem like many trees are involved, not just one as the OP suggested. And, inside, all of the structures such as ramps or platforms are constructed of wood rather than the stone of the
Ocarina of Time Forest Temple. Of course, they could have been removed, but why would one replace stone with wood? Stone would not have deteriorated between the two eras, as we can assume the time between the games can be counted in hundreds of years, and stone structures have been known to last thousands.
Now, let's check out Exhibit B: The Dungeon Maps:
The
Ocarina of Time Forest Temple Dungeon Map.
The
Twilight Princess Forest Temple Dungoen Map.
Notice that both maps are similar towards the bottom, with one central room, but that these similarities quickly disappear when the top of the maps come into view. Recall that in the
Twilight Princess Forest Temple, there is a large exterior room that leads to another portion of the temple that is large in size. This entire concept is completely absent in
Ocarina of Time. Plus, this combined with the open space of some of the rooms made the Forest Temple in
Twilight Princess have an open feeling, while in
Ocarina of Time it felt more like an ancient building with tight corridors.
(See the Twisted Corridor):
Essentially, the maps and feel, not to mention structure, of the Forest Temples are incredibly different, showing that the two are obviously different buildings and that the original Forest Temple from
Ocarina of Time is not present in
Twilight Princess as nothing even resembling it is seen. The Twilight Princess Forest Temple is its own structure that has not been seen previously in the Zelda series, as all logic and evidence shows.
Image credits for the Ocarina of Time Map go to Zelda Wikia
Credits for the Twilight Princess Map go to Gamespot
Credits for all other images go to ZeldaWiki