logical, i think so... we shouldnt be expecting this rom to work like other roms. Its leaked, thanks to some double agent deep inside Nintendo (Many thanks!).
What I think: The Master Quest is also part of the Regular Quest on the Gamecube. Because only the doungoens are different, the game take some parts from the same spot on the memory. Because this part of the game is so large, and didnt have any changes, they dicided to do this for the ending. Then, someone leaked the master quest to us, but it only has the parts that were in the master quest to begin with. The ending is so large that they told it to take it from the regualr quest on the same disc. Again, the only purpose of this rom is to experience the doungoens a second time, and differently. If you get to the end, its not any different (well, i dunno, working on finding that out on Gamecube), just the same ending! The different dungoens should be reward enough, and remeber, this isnt even supossed to be here, given its a Gamecube rom!