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

Yeah, it's inclusion in here is baffling because none of the listed issues have anything to do with the particular issue nixpkgs is having.