Comment by kmeisthax

The funny thing is, not only are there multiple Neutral endings, Toby actually wrote different variations of them for almost every possible combination of boss kill. They range from "you know, Alphys wanted to talk to you about something" if you killed nobody, to "if Sans ever figures out how to leave the Underground, he will end you". The latter is what you'd get if you misinterpreted "Genocide run" to mean "kill everything you see", which isn't quite it.

My guess is that Toby's intent was for you to play the game normally, get one of the many, many different Neutral endings, reset to get the Pacifist ending, and then a few years later come back to Genocide after hearing about this weird route where you get to fight the other font skeleton.