For mobile apps, though, you can bootstrap HPKP with a key built into the app. I worked on an app doing this, and it would certainly fail to connect in this scenario.
One solution is to use Name Constraints. The organizational certificate authority could be issued with Name Constraints limiting its power to a certain domain name only, e.g. *.example.com, using Permitted Subtree.
If I was setting up an organizational CA for internal websites (not MITM), I would consider using Name Constraints to limit the certificate's scope and potential for abuse or compromise.