The flatpak packaging tutorial has you build a cli app, so anyone building one is likely aware.

The real issue is invoking the commands. If you install a snap of top, you run top and it opens. If you installed a flatpak it wouldn’t be added to your PATH and even if you added the exports directory to your PATH you would need to remember to run org.gnu.top. Nobody wants to run some random flatpak run command all the time or create aliases for everything, so “flatpak isn’t for cli” becomes the mantra.

In an ideal world a flatpak could register the cli commands it wants to present to the user, and some alternatives system could manage which flatpak gets which command if there were collisions.