This is the approach that I've seen taken for this issue...you have to do all the work you would normally do in the NI.LV.Dialog app instance in the app instance that owns the VI from which you launched the Tools utility:
I will take a look to TS2 (as I'm a LV teacher, I also got all the stuff for TestStand... such a bad boy...) and process model customisation.
ShaunR, sorry for bothering you, maybe my question was too much "architectural" ... hum, you really are a nasty demon
Just kidding, thank you both for your help and advices.