Hi MOH,
as soon as you don't see MIR as "reverb", but as "virtual room", you will immediately understand that recording enineers usually have one "main" microphone array, which is used for all instruments consequently ("main" in the sense of "all microphones of the maÃn array", opposed to spot-mics). This is where much of MIR Pro's acoustic coherence comes from. In reality, you wouldn't be able to bring down the volumne of the rear outrigger mics for just the piccolo flute either. ;-) ... if you really _have_ to go beyond the possibilities of this quite natural implementation, you will indeed have to take resort to the workarounds I mentioned before.
But like I said - if you just need different RoomEQ settings for different (groups of) instruments, nothing will hinder you from applying them directly in MIR Pro!
... I still don't understand your "reload problem", sorry to say so. Why don't you just save MIR Pro's "engine settings" when you want to keep your already instantiated instruments in a different room ...? (File > Vienna MIR Pro > Save/Open) The settings for individual channels (i.e. Icons) can be saved, too (right-click > Save/Load) ... none of these actions will re-load existing sample-data of Vienna Instruments.
HTH,