We put that question to a SunRail spokesman.
"A third car is put on a train when the train is at 85 percent or greater capacity the previous day. Today, for example, the third car will be added for that afternoon turn. This is something that on-board personnel continuously monitor, as we do with special events. For example, the Maitland Arts Festival starts , so we will proactively add a third car in anticipation of additional riders. Something you may have experienced on board, some of our passengers prefer to stand rather than take an empty seat next to a stranger. The conductors do let standing passengers know of seat availability in other cars or levels of the trains when available."