The method of starting off with the blade lying flat on the stone is the way all butchers and meatworkers were instructed to sharpen their blades - it is the only way to remove those shoulders that the factories but on their knives as matter of economics. Prior to mechanisation and factory made knives most knives were convex ground and from all the information I have read on sharpening convex ground blades is to start with the blade flat on the stone or slightly raised. I was a knife maker and I made flat ground blades I made the knives with enough thickness so that they could be sharpened flat on the stone without weakening the edge at all. Scandi blades are sharpened in a similar manner except it is only the bevel that is laid flat due to their sabre grind. If anyone is looking for an authority on sharpening blades using this method go no further than the Razor Edge System devised by John Juranitch (I apologise to John for any mis spelling). Getting back to Knife Makers I am appalled at the number of makers who put all that time and effort into a knife with no consideration to the edge and profile of the blade. Many custom makers will actually use the Lansky system or similar to put the final edge on their blades - when I was making, as I said, I used a system similar to that espoused by John Juranitch in his book on Sharpening.
Unless you are sharpening safe queens, and who does anyway, whats a few scratches on the blade and if you want to avoid this you can sharpen down to about 2000 grit or use a compound on leather to get a satin finish. One of the great advantages of using such a system is that once you have done the original sharpening regular maintenance on a strop will avoid returning to the stones as much as other systems dictate.
Unless you are sharpening safe queens, and who does anyway, whats a few scratches on the blade and if you want to avoid this you can sharpen down to about 2000 grit or use a compound on leather to get a satin finish. One of the great advantages of using such a system is that once you have done the original sharpening regular maintenance on a strop will avoid returning to the stones as much as other systems dictate.