The most natural way of aiming the torpedo at a given point along the target is to aim the periscope at whatever point you want to hit as you are updating the range to target (upper right circular thingy). Updating the range using the stadimeter tool assumes that the target is XXXX yards ahead wherever the periscope is pointed.
So all you have to do is unlock the periscope and point it at the part of the ship you want to blow up when you update the range one of the times.
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