Let's put things in perspective. It doesn't matter how contrived and hard to find it was, and how cool the run was until that point. When you reach the debug menu, what every person will see is that you open the debug menu, use it to warp to the end, and done, which is incredibly lame because instead of "superplaying" you are using a debug function to warp to the end of the game. Debug code is considered off-limits for that reason. Claiming it's not cheating when the main purpose of a debug menu is to cheat is laughable.
I in some way understand people agreeing with this run because the extraordinary circumstances that allow you to cheat even though the cheat menu is hidden and disabled, and while it's a feat that deserves to be shown and that many people will find interesting, it has to be in a separate publication in a separate category. The any% Earthbound run should be, well, about beating the game, not about opening a debug menu and using it to skip to the end.
The fact that no judge has yet commented about the fate of this submission might signal that there's definitively an issue with this run.
Personally, I would settle for publishing it in the "concept demo" category, because it shows parts of the game that are normally disabled.