Think of a data flow A->B->C, with A e.g. handling incoming message server, B being a spam/virus filter, and C holding the user's mailbox. Spam/virus filters are useful, but are also rather vulnerable - so C is willing to trust B's spam/non-spam judgement, but wants to ensure that B can't alter or make up messages.

If protobufs had one canonical encoding, B could unpack the message and re-pack it when done; with the current protobuf implementation, B needs to keep the original blob around. In either case, C needs to check the signature on whatever blob it receives.

(Some details have been changed.)