Ah - the infamous "waterline". I saw that when I switched to using Slic3r (I used Cura earlier). The problem is due to lack of cooling on that layer. By default Slic3r tries to avoid using the fan if the layer time is longer than a certain amount, while Cura pretty much just runs the fan all the time. The "waterline" is the first layer of the Benchy which takes a while so the fan turns off, and the layer ends up deforming a bit.
Change the cooling settings so "keep fan always on" is set, and set a minimum fan speed of 50 or 60% and you should see the waterline reduce dramatically. 75% minimum fan should make it disappear completely.