I also prefer to process bit as they appear on the wire. A binary encoding is going to need different code for the parser/encoder. I don't see a problem tweaking aspects of JOSE that were bound to the particular JSON encoding.
While it would be nice in theory to be able to transform between encodings and have signatures still work, I don't think that is possible except in the very specific case where all that is being done is base64 encoding binary blobs. I don't believe that any canonicalization scheme has proved to be reliable enough in practice to actually provide the alleged value. There seem to be more corner cases than anyone imagines possible. I certainly would not want to break JWT for the sake of an encoding that JWT is not using.
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