Flatpaks can also be used to run CLI programs, but it requires using flatpak run <package.name> instead of using the apps standard CLI command. But you can create an alias and should work mostly the same way.
For example, I have neovim on my Debian laptop via flatpak. So in order to run it, you have to do
<span style="color:#323232;">flatpak run io.neovim.nvim
</span>
You can create an alias for that command
<span style="color:#323232;">alias nvim='flatpak run io.neovim.nvim'
</span>