just imagine a world where protobuf replaces JSON, would you really want that? you're not thinking big picture
Do I want protobufs replacing JSON? No. I want flatbufs augmenting JSON (and XML, and ...).
I maintain an ASN.1 compiler and run-time that supports transliteration of DER to JSON. This is possible because the syntax/schema language/IDL and the encoding rules are separable. This is how you get the best of both worlds. You can use optimized binary encoding rules for interchange but convert to/from JSON/XML/whatever as needed for inspection.
Ideally it is capnproto instead of protobuf, but in general the same applies.
It is a _transport_ protocol. You can still write your config or data in any format you like.