MIR Pro's so-called "Engine Project" data is indeed meant to save all Venue-relevant settings like Venue selection, microphone selection and setup, RoomEQ banks and so on - in other words: the "empty room".
All instrument-specific parameters are handled by the single instances of the MIR track plug-in, i.e. the "Icon" on a MIR Pro's stage. In VE Pro you can save and manage these settings by means of the so-called "Channel Sets". The respective commands are available from the context-sensitive right-click menu.
MIR Pro's plug-in version (VST/AU/AAX) simply relies on the preset management of the host. - Sidenote: The most important thing to remember in this context is the fact that the _very first_ instance of MIR Pro defines its output format (Stereo, 5.1, etc.).
... that said, we are _very_ aware of the fact that it needs a much more refined and powerful preset management to make use of a complex application like MIR Pro to its full extent. We work an update that will take care for these demands.
HTH,
/Dietz - Vienna Symphonic Library