Since my first visit to WDW in 1991 the MSEP and later Spectro always started at Town Square and exited in Frontierland near Splash Mountain--this for both performances. It's possible, however, that on special media occasions it ran in the opposite direction, probably so that Cinderella Castle could provide a backdrop for the parade to be taped or filmed as it proceeded along Main Street.
At Disneyland the parade's first performance generally proceeded from It's a Small World to Town Square, then reversed direction for the second performance, this due to the fact that the parade could not easily circle around backstage to it's starting point, as it could at MK.
Jim