stevec
FWIW you can use a SIT and multiple outputs. I do that for AD2 quite often where I'll start with a SIT, and if the project seems to need it I set some of AD2's individual kit pieces to separate outs than add audio tracks whose inputs are those AD2 outs. From that point I typically keep the stereo elements (cymbals, OH, Room) on the main SIT.
I've done the same thing for KONTAKT too, though I usually have to remind myself how to add outputs after the fact since it's not quite as straightforward as AD2... Unlike many others I actually do prefer to use SITs when I can; they've become a standard element for me. Fortunately I haven't had any real issues, knock on wood. 
Hmmm... OK I'm gonna have to try this later... Here's my thinking:
Omnisphere Simple Instrument Track
Load Piano in Channel 1, Bass in Channel 2, Guitar in Channel 3
Create 3 MIDI Tracks outputting to Omnisphere and have the channel of each be Channel 1, 2 and 3 respectively.
Make my Music.
"Oh but I want to add Guitar Rig on the guitar sound on Channel 3 without it being on all 3 sounds."
Add an Audio track, Add Guitar Rig to the FX Bin of that Audio Track, Set Omnisphere Channel 3 as the Input of that Audio Track.
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Still managed to use only one instance of Omnisphere reducing my CPU usage while still being able to add effects to only a specific instrument.
I don't have it up in front of me right now, so I'm not 100% that is all doable and would work, but I THINK from what you just said, that should be doable, right?