GNAT GPL removes the runtime exception, so if you build something with it linked to its standard library, it's also supposed to be open sourced. This means you can't (in a legal/technical sense, not a true prohibitive sense) make closed source software with it. FSF GNAT doesn't remove that exception, so it can be used in releasing closed source software.
That's the encumbrance that GNAT GPL imposes and FSF GNAT does not.