I've never played the multi-player game (you need a cartridge, link cable, and Game Boy Advance for every player!? balls to that!), so I've no clue if that dungeon or those enemies and tiles and whatnot are unused, but one thing I know for sure is that the HUD and Link sprites are different.
The original HUD had the rupees in the bottom left, keys in the bottom right, health and item at the top right, and your player number (ranking, possibly?) at the top left. The final HUD has some number at the top left (damn you uninformative IGN videos!), probably the player number or ranking again. The health and item remain in the top right, but the rupees were moved to the bottom left, and the keys have disappeared.
Here's a comparison of the green Links. The prototype Link (an unofficial pixel-isation of what's seen in the video is used here for better clarification) seems to be based off the Link to the Past Link, what with the brown boots and sleeves, and no tights; while the Link sprite used in the final is more based off the Wink Waker version, with the red boots, lime sleeves, and white tights.