The DMT comes flat from the factory and stays that way. No need to lap or flatten it. The thing to watch for is diamond wear and diamond loss, so easy does it as to use. Typically, they arrive aggressive from the factory and sort of mellow with use. Most I've ever done to clean it was go over the surface with an old toothbrush and water. Normally, I just rinse it off thoroughly, making sure there isn't any lingering stone residue after lapping or swarf after sharpening.

I don't have a Gokumyo, but I recall reading that lapping it is a bit special, involving less than a DMT or something. I'd study up on the question before taking a diamond plate to it.