The signing schemes I've seen used in binary protocols fall into two categories:
1. Canonicalize and sign: the format has a defined canonical form. Convert to that before doing cryptographic operations. If the format is well designed around it, this is doable, whereas JSON doesn't really have this and with many libraries it's hard to control the output to the degree that you'd need.
2. Serialize and sign: serialize the data as flat bytes, and then your signed message just has a "bytes" field that is the signed object. This is conceptually not far off from the base64 solution above, except that there's not extra overhead, since with a binary protocol you'll have a length prefix instead of having to escape stuff.
