Well, Flatpak installs aliases, so as long as your distribution - or yourself - add the <installation>/exports/bin path to $PATH, then you'll be able to use the application IDs to launch them.
And if you want to have the Flatpak available under a different name than its ID, you can always symlink the exported bin to whatever name you'd personally prefer.
I've got Blender set up that way myself, with the org.blender.Blender bin symlinked to /usr/local/bin/blender, so that some older applications that expect to be able to simply interop with it are able to.