We took a bus from the BC to the MK on the morning of 8/17 and the bus went straight from the BC to MK... On 8/14, when we traveled to the BC from the MK, the bus stopped first at the YC (right next door, no biggie) and then at the BC.
We didn't stop at the Boardwalk or any other Epcot resort on these occasions. All went very smoothly. Plenty of room, too.