The interfaces don't necessarily have to diverge wildly, but they do optimise differently. Many swipes and gestures can only be used effectively on a touchscreen, complex menus and arrays of small buttons need a mouse.

A good example is window management - how you handle that depends very much on your input devices. You could probably come up with a hybrid that added window decorations if you started moving the mouse around or something, but I guess it's simpler to just have two modes, and it's often possible to change window managers / configurations without even logging out of your session.