Hi there we did this last May. We found out the times the p and o express train tour was going and booked the same express train going.
we only did it in the previous port.
at the time there was definitely more than 1 express train running and it did stop at S.Pietro. We arrived just before 10 but left on a train before the p and o tour. - the tour got back to civitivecchia at 5.30 pm.
On a previous visit we took the Rome on your own trip which takes away the uncertainty. It used to have 2 drop off and collection points and still gave us plenty of time in Rome.😊