Because different universes (game, manga, anime) co-exist, and there are people who just love to make things more confusing.
At the very beginning, there was just Original!Red. Then the anime came into our lives and gave us Ash Ketchum. After four months, the first volume of the manga was released and Manga!Red made his appearance. Six years later, Fire (Remake!Red) replaced Original!Red for some reason. And recently, we got Origin!Red, thanks to Pokémon Origins.
Pixiv!Red just showed up at some point, ‘cause fangirls are awesome like that.
This is just my opinion. It’s really up to you; for example, there are ones who like to think Original!Red and Fire are the same person (“He just dyed his hair or something!”); ones who don’t acknowledge the existence of Original!Red (“OMG RED IN THE GAMES IS SO DAMN HAWT!”) (No offense to Fire fans…); or ones who don’t give a damn about other counterparts (“Game!Red’s first Pokémon was a Poliwag. Go read the manga!”). It’s a way to make the whole series more enjoyable, so as long as you’re comfortable with it, feel free to make up things~ :)
Probably because they’re not really the same person? I like to think that the Green paired with Pixiv!Red is a separate counterpart as well, as none of the others has green eyes and an Eevee or Squirtle (I’ve seen him with a Bulbasaur and its evolutions as well - no known other counterparts of Green choose it as a starter). He also has an unique personality, so why not make him a counterpart? :/
That works as well. In fact, I did think about that more than once :P
Red: Uhm… I remember catching a Krabby for the Dex, but it’s been in the PC ever since. Are you somehow mistaken?
Green: …Am I supposed to laugh?
"You’re so gay that it disgusts me."
"…So are you."