Oh my gosh that logo is unbelievably distracting! Especially when opening a page that "does ____ in real time" -- I spent way longer than I should have thinking "what is this logo doing and what does it have to do with the rest of the page ..."
The direction (inbound/outbound) comes from NextBus data and is frequently erroneous, so in that case a train traveling outbound is shown with the inbound vehicles.
The position above the last stop is because MUNI vehicles have significant extra track beyond the 4th/King stop that they use to wait and turn around.
It looks alot like something I did for my last job. Comparing schedules to actual transit bus performance. It's really neat stuff when you start digging into distance/time. http://imgur.com/gmN3EfS
This uses the same type of visualization as the train schedule in Edward Tufte's Envisioning Information: http://www.c82.net/images/java-railroad-lg.jpg