I rather like the trees and don't think that they need root lines. If nothing else, if there is snow, they would be covered up anyway. Besides, with the height of the camera, it would be just as likely that any exposed roots would be under the tree limbs as exposed around them.
As for the rocks, I see what you mean, but I would not worry about it. I really can't think of any way to clean them up other than perhaps using a much smaller brush to make the rock out lines and at this point, I would not bother. In any event, the existing lines match with the artistic style of the house and trees, so I don't think you need to worry with changing it the map at all (other than cover the outhouse... I mean come on... heh...)
Joe