This seems to change every few months. Sometimes the train will backtrack, Sometimes there is a change of trains at Millbrae. Sometimes the trains are clearly marked as Millbrae only and don't stop at the airport at all.

Right now there is a mix, including trains that are airport-direct and don't stop at Millbrae at all. And, of course, weekends can be different.

What I noticed most recently was the spacing of the trains kind of made it irrelevant which you took. The direct to airport train was 15 min behind the Millbrae/SFO train. So no real difference if you waited for the direct train vs. just backtracking on the Millbrae/SFO train.

I guess the lesson is to use the trip planner to see if there is a direct train running, else plan for the longer journey.