Why does running shellcheck from the demo flatpak work, but fail in Atom?

I've installed [Atom from flathub](https://flathub.org/apps/details/io.atom.Atom) . Now using the [linter-shellcheck](https://github.com/AtomLinter/linter-shellcheck) fails and says, the shellcheck command is not available. However, if I [use the flatpak demo application](https://flathub.org/apps/details/org.flatpak.qtdemo) and use [flatpak enter](https://unix.stackexchange.com/questions/500225/how-to-get-flatpak-enter-to-work/504144) to execute a shell inside of it, I can actually run shellcheck without any issues. Howwever, the demo applications has much less permissions than the Atom's flatpak. So how is this possible? Or, where is the error here? [MY question here would be obsolete](https://unix.stackexchange.com/questions/412869/how-to-allow-gui-application-in-flatpak-to-run-cli-tool/422438) if it just orked to run shellcheck in the flatpak. **Edit:** _Inside_ of the flatpak, here is where shellcheck and so on are: $ which shellcheck /usr/bin/shellcheck $ echo $PATH /usr/share/Modules/bin:/app/bin:/usr/bin (This is the demo flatpak, i.e. where I can execute it successfully.)