Technically speaking, in Animation Paper we have created one algorithm for doing the lines. The “Marker” and the “Pencil” is the same algorithm, the same technical settings, both of them goes down to half a pixel thick stroke – really the difference between the two is that the pencil has texture added to it. So if you need the pencil, but without the texture, then you use the marker. You can refer to it as the “mechanical pencil” 🙂 – it even fits with the shortcut M 😉
The lines in AP are simple digital representations – not the real thing. The marker and the pencil in AP ARE the same (except for one has texture and one has not).