Yes it "should" work; I've done it a good handful of times, sometimes via phone agent (when there wasn't enough booking class inventory for the extra seat so it would price higher; in that case you book the one seat online and they'll match the price for the EXST), and sometimes doing it myself online. I've never had an issue. In fact, one drawback of doing it via agent is you won't be able to check in online or even via kiosk, you have to see an agent, as they put an inhibitor in the record for some reason. But I think you'll save a small amount of taxes.

And don't forget to contact Delta after the flight to claim the Skymiles for the EXST (RDMs only)!