Haha, I contacted you earlier int he week re skim.
I've got the head off mine today too, and I have exactly the same. Pot 1 is clean and 2,3 & 4 are covered in carbon deposits. By any chance was the break in your HG on this cylinder?
I wouldn't bother TBH, it's not going to harm the performance in a noticeable way, plus any fine gouges/scratches created in the crown by scrapping can create a point of failure in the future.
As D4nny says scratches are a very bad idea as they can create start points for cracks in the piston.
I use ice-cream sticks and WD40 to clean off the carbon. No risk of scratching the piston tops. But always use the grease around the edges to catch debris.