It gives you flexibility in writing libraries while making it harder to design a new compatible runtime. That said, PyPy has achieved pretty good C extension support while making the language faster.
The claim was 'degrees of freedom in your language's design'. It's an odd one because the history of a bunch of similar languages has been exactly the opposite. Compare, say, JS to Ruby and Python. Even with the seemingly crippling burden of browser compatibility, Javascript has evolved out of its various design and implementation ruts a lot more gracefully than either Ruby or Python.