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).
kubeshark [0] is using ebpf to catch calls to openssl/go's tls lib and thus no need to juggle certs. Has pros and cons compared to your method, but an interesting comparison.
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