They are talking about the Jefferson Y chromosome appearing in a male line of descent from Sally Hemings (her son’s son’s son, etc) Whether it was Thomas Jefferson, president to be, who contributed that Y chromosome can not be proved or disproved - but a Jefferson was the father of that line.
Well, no, read the article again, they were attributing it to the Carr nephews and the only way they’d have a different surname would be due to their mother being the Jefferson, not their father. Unless, that is, they actually were fathered by a Jefferson male but adopted by a male of a different surname, and that would have been highly unlikely in such a prominent Virginia family.