I...don't think that that was the plan.
They were going to release a disk expansion for the 64DD called Ura Zelda, with new content, namely new Temples(Like Wind and Ice) and Side-Quests. It was scapped though, but booting up OoT an a 64 with a DD attached will display the Ura Zelda logo and ask for Ura Zelda.
The Wood Temple was most likely existed sometime in OoT's developpment, but as a normal dungeon, not an extra one only playable when the game was done. What are your sources? I may be wrong.
I've played the OoTMQ Debug, and those cut rooms are generally beleaved to not be part of the Wood Temple (seeing as there's no wood in any of them). I think that it was part of a cut Stalfos dungeon (similar to the Skulltula Temple), but I'm probaly wrong.
Anthor cut Beta room on the Debug ROM ended up being the MM Final battle room. It's a really interesting ROM, but I'm not sure about Nintendo's position about it being freely avalable (I think it should be, as it's the only way to make new maps for OoT).Valve let the public play the beta for their game Half Life 2 when it was leaked, I think Nintendo should the the public play the leaked OoT debug.
But now I'm just rambling.