Because between Link and her they have all of the Triforce pieces needed to open the gate! What you do in Level 3 is try to get to the gate.
Er ... right. Then we are on the same wavelength on that one then.

Also, I said that the Dark overworld would still have locked gates and treasure chests and such, and should be considered an outdoor extension of Level 3. (Not that there'd be a map and compass for that area, though.)
Well, perversions don't necessary add chests and such to them. :p There are chests and treasures in the Temple of Shadows because the monsters stole everything (EVERYTHING) from the temple of Light and brought it into the Temple of Shadows. That's why there's junk just lying around. (Junk, including puzzles, chests with keys, really big chests with blinding arrows in them, etc. :p )

Besides, not having it as an extension just makes it faster to build. All we need to do is copy the area structure, add little obstacles so that it's a fairly linear area, and make the occasional Zelda encounter where you see her pop back in and then she pops back out; discovering that she's been perverted on your third encounter. Then you fight her when you see her next.