So, it turns out that flatc has a (seemingly undocumented) option to generate the schema as a JSON. This introduces the possibility of writing a pure Julia compiler for flatbuffer schema using only existing parsing packages. You can see an example JSON schema here. I've not yet validated that it's complete (i.e. the full Julia code can be inferred from the JSON schema only), but so far it looks ok.
If #51 turns out to be a real disaster, I might start working on this.