It’d be dangerous if an installed app claimed to be something like sudo or bash. Even if a mechanism was created for flatpak apps to claim a single shell command, there is no centralized authority on all flatpak apps to vet them. If there was for flathub, and each uploaded package was checked, that still leaves every other non-flathub flatpak repo which must implement the same vetting. Because there’s no way to guarantee to do it safely, and because flatpak devs are unwilling to compromise, this is just what we get.