Here's an interesting discovery, tested both on a Surface Pro 2 and Surface Pro 3.
If you hide the menu bar (View -> Show/Hide Menu), scrolling with the Type Cover's touchpad works just fine. Scrolling by using a finger on the touch screen still selects, rather than scrolls, however.
If you hit Alt to show the menu again, you'll find that scrolling in the main window doesn't work either. This makes me think that the menu eats the scroll events, instead.
However, as a work-around, hiding the menu will work.