When designing the AR3 I tried to make as many of the components as simple as possible and out of standard thickness plate material where possible. Keeping the J2 arm and J3 motor mount as simple as possible meant the J3 motor shaft would not be exposed very far. I wanted the design to use all low cost off the shelf parts but I had trouble finding an off the shelf belt / pulley combination that would work with the limited shaft exposure so in the original design I chose to use a 6mm roller chain and sprocket as this would fit the shaft length and handle the needed torque.
More recently I have designed a custom pulley and belt combination for the robot.
The Annin Robotics hardware kit comes with the newer belt and pulleys but I wanted to leave the chain and sprocket in the manual as an option for those building their own robot and wanting to use off the shelf components without having to purchase a hardware kit.