Missing from the "hidden from the user" argument is the fact that .config, and dotfiles in general, are also hidden from the user. It's not the defining distinction that one may think it to be.
Command-line binaries are also typically installed at locations hidden from the user (/bin, /opt/homebrew, ~/.bin, ~/.cargo/bin). Further indication that the "app"-oriented Apple documentation is intended only to apply to "apps", which are installed at /Applications or ~/Applications.