I'm a fan of the writing style. It reminds of smart people I know. I haven't bought any fly.io yet, so I don't know that I'm you're target market. Still--well said, repeatedly.
I wish I could tell you it would eat a bunch of your time, engaging your curiosity and sense of wonder all the way, but really what's going to happen is you're going to install `flyctl`, go somewhere with a Dockerfile, do `flyctl app create` and then `flyctl app deploy` and it's going to just work. :)
Have you considered using ssh command's ProxyCommand option? It allows you to replace the TCP transport with communication over stdin/stdout.
It could help you replace the TUN with something more cross platform, and possibly with less overhead. You can pass in the hostname using %h, so you can even have virtual DNS.