With ubiquitous use of TLS and the advent of certificate pinning Wireshark is becoming less and less useful. Even if you convince the phone to accept your man-in-the-middle certificate with a provisioning profile, there's no way to proof that it sends the same data as if it got the real certificate.

If iOS was changing the data it sent out depending on which root certificates were installed, that would be a huge scandal, as I cannot imagine _any_ non-malicious reason to do that.

That's not proof of anything, but again, at some point I feel you have to assume good faith. Apple does not have a history of doing stuff like this.

Exactly, you're assuming good faith. Instead it should be proven good faith.