I am confused about the reproducibility of a system through flakes

Bit-for-bit reproducibility is a very high bar, and while projects like https://reproducible.nixos.org/ attempt to tackle this and binary caches can hide/mitigate/shim bit-for-bit-style reproducibility, the use of nix alone is not sufficient to claim bit-for-bit style repro, especially because many build chains and software are not written to be easily bit-for-bit repro. See "NixOS is not reproducible" for more details and perhaps a better place to actually have the discussion if more commentary is important. I’m only commenting in this thread because I think as a community it does a disservice to advertise claims that later do not prove out. That can cause a lot of loss of faith in the ecosystem.

Nix does provides dependency-graph reproducibility, as you note, which is already great for most practical purposes and very hard to achieve in other ecosystems. A great win! Definitely a huge reason to use nix, and I don’t see a better tool currently.