No, HPKP is not intended as a mechanism to prevent that. In fact, all user agents I'm aware of do not check pins if the certificate chain leads to a custom CA certificate (one that has been installed manually, as opposed to the default root certificates the user agent ships with). (I believe this is a MAY in the RFC, but all major browsers have implemented it that way).

Mobile apps typically have other key pinning mechanisms that are preloaded (i.e. baked into the binary), but that's typically easy to bypass if you're the owner of a device; it's not really effective as a mechanism against reverse engineering.