>>715396251Because obviously the game's main route is going to be the one that ties into the canon of the original game. The pacifist route is the main route of Undertale, the rpg where no one has to die, and Undertale Yellow is meant to be built off of Undertale's design, albeit with certain differences here and there.
Let's be honest, most people play UT/DR, and by extension, UTY by playing along the game's extremes, either true pacifist or true genocide. The neutral routes/endings can be interesting and have stuff worth seeing in them, but they usually don't have a whole lot going on that justifies playing the game like that. It's like playing Mass Effect 2 and 3 while doing paragade, it's just not really worth it.
With that in mind, if people are mostly going to be playing the game by strictly adhering to one path or another, it makes sense that the "canon" or "true" ending would be on one of those paths, not just in one of the various neutral routes.