The Federation Cruiser's Artillery Beam fires automatically without allowing you any targeting preferences. I've had it cut through most rooms of the enemy ship, or just a few. Is there any means or method to how it chooses to lay the line of it's beam or is it random? Is there a minimum\maximum number of rooms it can hit?
From the wiki:
Since the beam fires automatically and randomly, it can strike multiple rooms or just one.
This gives you an advantage against larger ships as the variance between two randomly selected points will be larger, which means the average difference will be higher, which of course means you have the potential to hit more rooms, and thus do more damage.