It wont optimize the waypoints automatically because that would take route control away from the driver. Supposed you needed to hit destinations in a certain order. If it optimized automatically then you would have no control over where you wanted to go first (if you have a preference). I'm pretty sure there is an option button to optimize the route after you input the waypoints.
I'm not sure it does it automatically but you CAN still set preference in the waypoints menu. I went to my car and played with this before I wrote anything in my first post. On the upper right is the optimize button and the lower right you can change each individual waypoint up or down in preference with your destination being at the bottom.
2014 Mustang GT Premium,6M,Black,401A Brick Red w/ Cashmere Accent, Elec Pkg, Rev Cam, Comfort Pkg
Ordered:12/18/13 VIN: 01/21/14 Window Sticker Online: 02/04/14 Scheduled: 01/21/14 Built: 02/10/14 Original ETA: 02/25/14 Delivered: 02/17/14 Home: 03/08/14