base64 is an encoding, and a base64-encoded PNG is still an image. Factorio blueprints are base64'd deflate'd JSON with a small single-byte header[0].
It would be comically trivial to setup a .gitattributes filter[1] to do the conversion for you on checkout (to the base64 form) and commit all JSON, allowing for beautiful diffs.
It's a bash one-liner[2] to turn JSON into their base-64 form and into your clipboard anyways.
Most tools operate on the compressed, binary header including, base64 encoded blueprint strings, not the raw blueprint JSON payload.