For the parameter part of ResourceContainer allow_message_fields would always be False, since MessageFields in a path or query parameter wouldn't work (at least I can't see how).
For the request body a ProtoModel is created first (with allow_message_fields parameter which would be True in this case) and then passed into the ResourceContainer where the parameter fields are created (again with allow_emssage_fields=False) (See line 1345 above).