Sounds like the bit-packed protocols save bits (that's clearly good), while the other protocols are self-documenting. Documenting is good.
Why can't we have both? Something like protocol buffers (yes, Raymond mentions them in the article) is a binary protocol that makes pretty efficient use of the bits on the wire. But they are also very well documented. And it's "documented" that is useful, not "documentation is included in every message that gets sent".
Is it possible to look at the on-wire protocol and tell that this message uses protocol buffers and which protocol specification it is using? (I'm not sure. I hope the answer is yes.) Is it possible to find the documentation for a particular protocol buffers specification once you know which one it is? (I think it is, if by no other means than a google search, although a more automated repository might be nice.) If both these things are true, then we can have bit-level efficiency AND have well-documented and extensible messages.