The main issue is the handling of security updates within the Nixpkgs ecosystem, which relies on Nix’s CI system, Hydra, to test and build packages. Due to the extensive number of packages in the Nixpkgs repository, the process can be slow, causing delays in the release of updates. As an example, the updated xz 5.4.6 package took nearly 5 days to become available in the unstable branch!
Fundamentally, there needs to be a change in how security fixes are handled in Hydra. As stated in the article, Nix was lucky to be unaffected, but multiple days to push out a security patch of this severity is concerning, even if there was no reason for concern.
After thinking a lot, your stance does make sense. However, it is not for the points you’ve raised in your defense - they’re not strong reasons that support Nix’s flaw, if we are talking about a generic trojan. The store-based file hierarchy would serve as a sort of defense, however, it isn’t a fool proof security.
However, if its solely targeted keeping Nix in mind, then yes, it’s a pile of stinking mess, with how the entire nixpkg file is filled with diff files. Diff files are not only difficult to read, it is also very easy to inject code without anyone finding out. It’s a ticking bomb waiting to explode.