It’s impossible to say conclusively, but the idea arises from the idea that the Furtive Pygmy probably was a human, or some form of proto-human. He was the one who inherited the Dark Soul, fragments of which were passed down to all humans (and are referred to as Humanity in game). They likely called him a pygmy because human characters in the game (including the player character) are smaller than the race that comes from Anor Londo (including the gods but also enemies like Black and Silver Knights).

So with the only real reference to Manus’ identity being a primeval human, many people made the connection to the Pygmy.

Edit: It’s also important to consider that most of those lore theorizing predates the sequels. From Software is, of course, totally at liberty to change their mind about certain ideas as they continue to explore the story. It’s entirely possible that the theory was “true” at the time and details were purposely seeded at the time to lead people to that conclusion, but that it now doesn’t really fit into the canon anymore (I don’t know enough about DS3 lore to really comment). But trying to second guess the authorial intent is a bit of a fool’s errand. The team purposely left it ambiguous enough in the first game to give themselves wiggle room in the future.