Agree you should be able to choose your interrupts. I think the Colour option for message log should have a checkbox, which determine interrupts, on interrupts. It should be easier for a quick check to determine whether to interrupt or not. Nothing worse then forcing an auto to bypass and interrupt you trying to get past, but missing an interrupt you really want to stop at.
Example in battle thermal contacts from missiles that are miles away when you already started the battle and got your auto launching enabled, if you could turn new thermal contacts off and then run your autos then I never get that problem where I force turns only to miss other stuff.
This should be a definitely be option.