> The fact that an empty message can successfully deserialise into any valid protobuf is an insane decision and should have been thrown out long ago

The reason for this is that the protobuf wire format is designed for very high entropy: It contains only a minimal amount of metadata and consists mostly of data. This means you can deserialize most wire messages as a different message. This is a tradeoff: smaller message size for loss of schema information. This just means that schemas need to be handled at a higher level. This tradeoff makes some sense if you process millions of protos per second.

BTW: Dismissing a tradeoff like this as insane is derogatory. You can do better

This is the main drawback I also experience with zero values, knowing whether something was set or its the zero value. Like I said, there are some work arounds, buts its a tradeoff. Perhaps its a tradeoff you don't like.