Yes, that option was originally there to turn Bluetooth over MIDI off for security reasons, but pretty much only developers would know how to communicate with an H9 using Bluetooth over MIDI anyway. We have added an option in the v1.6 release that allows you to select a Core MIDI device and send its data to an H9. This release isn't out for iOS yet, but that feature will let you do things like connect an IK Multimedia BlueBoard or a Livid Instruments Guitar Wing to an H9 through H9 Control. It will also let you connect the output from another app to an H9 through H9 Control.
What you're describing is a little bit different though. You'd like H9 Control to create a MIDI input port that could be connected to another app and have H9 Control run in the background sending the MIDI data over to the H9. We'll have to think about that. It's not currently supported and we haven't considered that option up until now.