That has nothing to do with flakes. When I add a "module" to my repos its the same. I have to add it the git repos or nix does not "see" it. And yes, its pretty unintuitive.
> 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...
(Which is totally valid btw)