I know that a lot of what Nix does is working around its break from FHS, but I can imagine there are still things that seep through. Are there any unsolvable problems due to this?
I saw on this post that it is possible to use FHS on Nix. Does this solve all potential issues then?
Because the nix package manager places all system packages under
/nix/store/uniquehash-packagename-version/
Where the unique hash is obtained via a Merkel tree of all the inputs. So in particular, binaries and libraries exist underneath those directories, not in the places you would expect from FHS.
In order to make the system actually work, environment variables are set up and executables are patched to refer to specific paths within the Nix Store.