Protocols in general cannot be obfuscated directly with this technique. For the sake of simplicity, I will assume we are talking about network protocols. Becaus

Protocols in general cannot be obfuscated directly with this technique. For the sake of simplicity, I will assume we are talking about network protocols. Because this encryption, by definition, does not change behavior, the program would send identical messages over the network, and you can still monitor these and reverse engineer the protocol like before. For the more general, but not formally defined, idea of obfuscation you would also be able to obfuscate the network traffic and other external stuff, because you can change the behavior without actually changing the behavior.