I think you are talking about these two spots (about 30x magnification). The seller was right, there is nothing to be concerned about. I guess the stone is very old and a bit weather-beaten at the surface. It just needs a good lapping. I recently moved and i am just unpacking. But soon I'll test the stone. My kitchen knife was definitely extremely sharp with it and there was nothing toxic in the stone.
Yes those are the spots. I figured they were fine, but he made me and others uneasy about it. He had it on his site then pulled it because of those spots. Then offered it to people without putting it back on the site and then put it on eBay on his alternate account and shut down his site for a month. He did it right before I could use my 25% discount too. He needs to stop being so shady. I think you got a great stone there. I almost bought it myself several times. He sold me a wonderful stone as an Ohira, but it turned out to be a Nakayama. Not going to complain on that one. I think his wholesaler is spot on with which mine for some stones and way off with others not always in his favor either.