It makes a lot of sense for a wire format to save space by having a default value and omitting the message when the value is the default, and by standardizing on a specific default, the protobuffer protocol avoids developers having to wonder what the default is for every field.

I agree that it can be a sharp edge for the tool if you don't see it coming... It can be convenient to deserialize a protobuffer into an in-memory representation for working with it. Proto doesn't do this for you because it would be unnecessary overhead if your code can just work with the protobuffers as-is, and protobuffer errs on the side of speed.