I would be shocked if GitHub's lawyers didn't argue that using copyrighted material as training data for an AI model is highly transformative. There may be snippets available from the original but they are completely divorced from their original context and virtually unrecognizable unless they happen to be famous like the Quake inverse square root algorithm. And I think GitHub's lawyers would also argue that Copilot's use does not affect the _original_ market -- e.g. it does not hurt Quake's sales if their algorithm is anonymously used in a probably totally unrelated codebase.
Your counterexample would probably fail both tests -- it's not transformative use if your software hands out complete pieces of copyrighted software, and it would definitely affect the market if Copilot gave me the entire source code of Quake for my own game.
[0]: https://fairuse.stanford.edu/overview/fair-use/four-factors