Configuration I think is a carry over. At C2 first inception C2 was going to support multi export to various languages nativly(JS, C++, Java, ObjC...). However that was dropped real fast. So Configuration doesn't do anything and probably won't in the years to come.
As for Touch. Since Mouse also simulates Touch input and Touch will react to Mouse input. I suggest use Touch for all Left Click based actions. You only need Mouse when you need the active mouse location for say "is mouse over", or other mouse buttons as in Right click, scroll wheel so on.
I took over a project once that used Mouse only, but was some day going to be a mobile game. Slowly over a week I modified all the Input to Touch. Except that I left key elements where I need the Mouse X/Y when I wanted an object to follow or highlight the button. Worked fine. When I ran the game on mobile device. The game still ran fine. Except I didn't of course have any mouse features.