Everything is much more efficient with binary format like protobufs or flatbuffers. And if the format has a schema, the schema is the documentation, an d you do not need to have comment in the config file itself.
The main benefit of a flat file format for configs is that it can be added to source control and edited by any plaintext editor. If I kept config as protobuf, I would need special tools to handle it, which could be annoying (e.g. if I'm remoted into a remote system). It would also make it more difficult to see diffs between different config versions stored in git.