Certificate pinning would defeat this. Bake it into your app that you only trust a specific certificate regardless of what is in the system trust store.
Certificate pinning is inherently security by obscurity; it's intended as an annoyance for anyone trying to reverse-engineer the service, rather than an insurmountable barrier.
Certificate pinning is one of the most user-hostile security inventions we've created. It makes it so hard to get access to the traffic coming out of your own device, which heavens, seems like such an elementary ask.
Not if you control CAs. Cert pinning only works in a limited amount of cases, and certificate transparency only works with CAs who have agreed to implement them (Which is not the vast majority).
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