I have followed Misterio77’s minimal config example to configure my system (flake & home-manager). Initially, I expected home-manager to get installed when running nixos-rebuild switch -v --show-trace -L --flake /etc/nixos#hostname. That did not happen.
[When using flake.nix] The Home Manager configuration is then part of the NixOS configuration and is automatically rebuilt with the system when using the appropriate command for the system, such as nixos-rebuild switch --flake .
Enable programs.home-manager.enable. In the HM doc example, that would be done under home-manager.users.jdoe, say, inside home.nix.
However, proper answer comes down to what your use case for home manager is:
If you have a single machine NixOS where you want to use both NixOS options and Home Manager ones, you don’t need the homeConfigurations output at all.
If you have machine A on NixOS and machine B on a different OS but you want to use same user config across all machines – you would need to reuse the modules(same home.nix as an example) in homeConfigurations output by importing them in the flake.nix.