The laser looks though the transparent bottom of the CD, but the layer with the pits is just under the top surface.

Ah, well, in that case I apologize; I thought he was saying that it is the top surface that is etched. That would be "right under" the Sharpie markings.

You say "just under". That is a little more ominous. How far is 'just'?

If I mark my finger with a Sharpie, the markings don't injure or dissolve my skin. Whether I leave them there two minutes or two weeks, they come off with a little soap and rubbing, and afterward, there's no damage to or change in the skin visible to the nekkid eye. Difficult to imagine how they could permeate tough plastic.