There is an ‘option’ in Cubase, which doesn’t seem to be saved with a project when unchecked, and which I would like to have unchecked permanently. But I cannot find where to do that, It’s called Remote-Control Focus (associated with Smart Controls) and it can be seen by clicking on the little icon at the top right of the Instrument Rack. I went through Preferences and also Quick Controls in Devices. Have I missed it, and can it be deselected permanently?
So the answer is that no one, including Steinberg, knows how to do this?? 
I would love to know this too!
Yay!!.. Cubase 9 and it’s still not being saved with the project!!!
Let’s see if in 2018, on cubase X, we will have this thing saved with the project!