I took direct flight once and never again. It counts only as one segment.
I did TPA-CLT-BWI and had one boarding pass. At CLT I had 1:15 minutes so I've decided to go out and smoke. On the way back, TSA agent asked me to give him correct BP when he saw Tampa to Baltimore on the stub.
I've told him that this is correct BP. He just noded and let me go.