So instead of extending QR codes, which are inherently binary, to efficiently handle binary payloads, we invent yet another ASCII-based tunneling scheme. Why ever fix any problem when we can just pile workaround upon workaround upon workaround?
Becaus sometimes you need your solution to be used be the public, voluntarily. If they have to install an extra app to read your "looks-like-QR-code-but-not-quite" thing, then you have at least an increased risk of not getting the adoption you want to get. This is not a realistic choice for many projects.
If not, there is a software layer anyway. Adding another skin to the onion is not the best way to compress data.