They will check you in for AF or KL flights. Why would they not? At ATL, DL checkin counters ARE AirFrance/KLM check-in counters.
Well, they DO actually have separate counters, so I don't think you can say they're the same. I've always checked in for Air France at the Air France counter in the Int'l Terminal; it seems kind of pointless to have separate counters if DL can do it all. Have you actually done this, i.e., checked in for an Air France flight at the DL domestic counter?