The reasoning beyond that is all viewable in the category discussion thread from like the week the game came out.

The general consensus was that since true Any% involved no escape rooms (unlike any% from all the other zero escape games) and was literally just waiting for cutscenes to go by with the occasional password fill-in it was rather silly to have that be the "main" run since improvements literally consisted of having a beefier computer or filling in text boxes marginally faster and made for an incredibly boring, shallow run. And I say this as someone who ran that run just for the heck of it.

That route only has the most runs because it's really just that easy of a run. There wasn't a large incentive to argue intensively about the run layouts because no one runs this game in the first place.