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But no one even knows it exists other than Red and the scientists who helped birth him.
The same started with Mew, Mew was so rare it was considered to be a mirage because no one had literally seen them. it doesn't matter whether they were seen only that they are beyond rare, have uber Powers (Dialga/Palkia being idols of time and space), and or changing the world in some way (Regi)
Only insecure and ignorant people try to debase someone online based on their username.
Perhaps it's legendary for its sheer power and capabilities? You're trying to apply too much logic on a basis which the game does not supplement too well towards. We'll just go with some of the gameplay aspects that consider it "legendary"
- High BST (Don't come at me with Slaking..) - Only one - Origin oriented - Presented as one of the strongest Pokemon in the entire world