Because the plugins are separate from the base program, the answer is a mostly confident "yes."
What I've done in my MMF days is call controls from an INI. That allowed me to not only offer full customization to the player, but also pass along any key to any function in the program. Unfortunately for now, Construct's behavior controls are locked into each application's default controls. I believe it would be a nice, temporary work around if maybe Ashley or Rich could modify the plugins to accept controls from an expression, untying them from the defaults. The fancy UI could come later.
Any devs listening in? It could go something like this.
[code:2jw0ex3c]//User Defined Control at Runtime
+Keyboard and Mouse: User clicks on button "Set 'Jump'"
-Set INI 1,1 to (capture next input)
-Set Global Variable "P1_Jump" to (INI 1,1);
+Keyboard and Mouse: (Global Variable "P1_Jump") is pressed.