It actually is specific to flakes. Classic nix commands can see untracked files just fine. Flake evaluation behaves differently because of how it decides which "scheme" to use:

> If the directory is part of a Git repository, then the input will be treated as a `git+file:` URL, otherwise it will be treated as a `path:` url;

This is why untracked or unstaged files disappear when using flakes:

https://github.com/NixOS/nix/blob/ec6789f9dafce41011418fe6fc...