Jeff should come back soon, we have a couple of good ideas about improving SI :)
With your need for complex application identification your only option is to combine SI with AutoHotkey. You could set up SI to identify the application at first level (eg. firefox.exe or whatever) and delegate the actions to a AHK script that is able to do further filtering based on window class/title/group and trigger the desired action. Not a simple goal to achieve, nor is the task an easy one, but until Jeff returns I don't see any other way.
As for the disabled gestures, Cerberus is right, I'm using that strategy myself. You don't have to assign a Command for every single Action you create. I have Commandless Actions named Disabled Gestures in some of my applications that collect gestures I don't want to do anything in that specific application (technically it overrides those in Global Actions) . Exactly the "passthrough" type action you need, one with no Commands at all. Sometimes the most obvious solutions are the hardest to recognize :)
