It is arbitrary, when I started to learn this game the rule was already like this, I just did a run within the rules to post on the leaderboards but I have a real Any% run (ending 1) on my youtube channel.

Runer-ish here. Xeno was the first person to run this game and so chose this rule, why exactly i couldnt tell. Maybe since the 2nd and 3rd ending are "harder" (not really anymore since we can still keep the object needed towards these endings with a skip) to get than the 1st which his just completing the game. Maybe an ending one category should be added or the ending 2 and 3 should be an entire new category while ending one become the any%