I also got the same feeling from that, in fact, I would go as far as to say that nixpkgs and nix-commands integration with git works quite well and is not an issue.

So the phrase the article says "Package managers keep falling for this. And it keeps not working out" I feel that's untrue.

The most issue I have with this really is "flakes" integration where the whole recipe folder is copied into the store (which doesn't happen with non-flakes commands), but that's a tooling problem not an intrinsic problem of using git