Yep, certificate pinning is the one scenario Subtrace can't handle in my experience, but thankfully, it's fairly rare like you said. And IMO there is no general solution to the problem [1], but it's one of those very interesting problems to daydream thinking about when you're stuck in traffic or whatever :)

We still try our best by handling as much of the long tail of environments with some library/framework specific workaround (e.g. Deno bundles all TLS certs in its binary so we set the DENO_CERT env var when applicable).

[1] https://news.ycombinator.com/item?id=42923998