But isn't this exactly why certificate pinning is needed... Sure I can roll my own PKI and install the Root CA on the client devices, but they can still intercept their own traffic by installing their own trusted Root CA.
Certificate Pinning is the solution you'd look to if you have a clients that cannot securely ship with root certificates/cannot pick the root certificates they will use to validate a certificate when initiating a TLS connection.
Edit: I should add that I am not a mobile developer, so I don't actually know if the 'bring your own root CA' method is supported by the corresponding TLS libraries. But I know that this is possible 'in general'