Yes, starting in the afternoon the bus route does change. It will pick up at DTD and PI first, before heading to TL and then to the resorts.
In the morning, the buses stop at TL first due to guests trying to make park opening, arriving early for seats, etc. It's all based on "whos going where"... more people board the buses in the morning for TL while more people in the afternoon board the bus for DTD and PI since the water parks are just about to close. It's easier to drop people off at DTD first in the afternoon to clear up some room for those leaving TL around park closing. There wouldn't be enough seats if the buses went to TL first.