As the Great Cannon is a model representing a real cannon and crew, I believe you should be able to 'imagine' or allow for a degree of trajectory in the cannon's shot, allowing it to fire at larger targets in the distance aka over walls, hedges, troops on lower ground or through enemy troops and so forth.
With the 2 additional dice rolls being representative of the unpredictability of aiming a cannonball, the main idea being that the target; say a giant in full view but far away, is what the crew are aiming at. Yet the placement of the first marker is a representation of the combination of the amount of powder, muzzle trajectory and wind etc. factored by the crew to hit their original target the giant. In reality the crew of a cannon wouldn't be thinking 'Okay if we aim at that orc in the third row of that unit we might get a good bounce and take the giant's legs out, as long as we don't put too much powder in, in that case we dont really want a large bounce'; they'd be trying to range in a shot on their target by seeing their results of probably their first and second shots. If shots fired by a cannon hit interveening enemy troops along the way I see no problem, they are the enemy after all.
However, I do believe firing through or over your own troops at any range is rather out of hand (for an empire army anyway) as is shooting troops that are out of the cannon crew's line of sight behind terrain etc. Ultimately a cannon is a long range anti personnel weapon designed to plough through large formations of troops, usually deployed in batteries in the centre or in between formations of troops. Showing that they didn't have the capibilty to fire over large formations of friendly troops. Howitzers/Mortars on the other hand are perfectly capable of firing over their own troops.
