Apparently, HP has provided no evidence on any lack of microscopic scratches on the crystal, as you stated - it was a claim by an art restorer who also claimed that it came from Atlantis, and that the Knights Templar carried it around.
Since then, it seems that it's been realized there were holes for support pegs drilled into the crystal by metal tools, and 19th century jewelers tools were used in the carving of the teeth.
It all seems like a bunch of hogwash to me.
http://en.wikipedia.org/wiki/Crystal_skull