In Nix, "system" generally refers to the cpu-os string, such as "x86_64-linux".

In Flakes specifically, these strings are used as attribute names, so that the Nix CLI can find a derivation for the right platform.

Many things, such as packages, can exist on multiple systems. For these, use the perSystem submodule.

Other things do not exist on multiple systems. Examples are the configuration of a specific machine, or a the execution of a deployment. These are not written in perSystem, but in other top-level options, or directly into the flake outputs' top level (e.g. flake.nixosConfigurations).

Such top-level entities typically do need to read packages, etc that are defined in perSystem. Instead of reading them from config.flake.packages.<system>.<name>, it may be more convenient to bring all perSystem definitions for a system into scope, using withSystem.