NOOOOOOO. Don't do that to a Koster. Here's what I would do. I like to put a very micro micro-bevel on my scandi's. I freehand but there is always a place for the Sharpmaker in my opinion. What I do with scandis (done it with Mora, Roselli, Helle, Brusletto) is set up the Sharpmaker on the 30 degree "back bevel" setting. About 50 strokes on the edge of the brown rod, 50 on the flat side, then repeat on the white rods and then strop.
The microbevel will be so small that you'll have to hold it up to the light just right to see it, 30 is still pretty acute so it will cut well, there will a "more steel behind the edge", and it will be easy to maintain without going to great pains. This of course could be accomplished free-hand by laying the big scandi bevel flat and tipping it up a few degrees.
No the other option, IMHO, with a nice scandi like a Koster would be to re-do the whole bevel scandi style by laying it flat on the stone. What that will tend to do is create a very subtle convex shape as you just cannot hot it absolutely flat...it will rock a bit. For very hard knives (and I don't think Kosters are) it is recommended to sharpen free hand because that tends to give the bevel a bit of convex.
In addition, from what I understand, Kosters are a little but convex anyway...like Rosellis are...sort of a hybrid between scandi and convex with the bevel almost flat but not quite.
What are you cutting? Do you have a CPM 3V model?