My understanding is like this. For multi-user computers, you’d manage packages with home manager. If you’re developing a project or need some kind of specific built tool or dependency, define in it in a flake.nix or shell.nix or build.nix in the project folder. And for single user computers, or maybe admin accounts install at NixOS configuration.
Whats the intent for each location? The current question Im asking myself is “why install home manager when Im on a single user instance and can just update configuration.nix?”
I wish you could config defaults for zsh/nvim in the Nixos config. I have some servers that are generated from a config file and then meant to not be managed after that (so I build a sd card for them and insert card and they are booted into a working system. If a configuration needs to change, the idea is that I rebuild the sd card rather than rebuild on the server.)