Let's see... You're standing on a raised mound throwing down to a target. Is there anything meaningful about aligning the shoulders with level ground? I don't think so. If anything, your shoulders should be aligned downhill since that's where you're throwing. On the other hand, there are lots of pitchers who don't do this either. Andy Pettite, for example, aligns his shoulders uphill. Now although he's managed to get good at pitching that way, I wouldn't recommend it.
Since you need to get your hips going down the hill to build up momentum and get into footstrike quickly, it makes the most sense to me to align yourself in that direction.