The song was written as the opening number for the movie, The Harvey Girls, staring Judy Garland, who sang it.
The movie was set in a much earlier time, late 19th or early 20th century. It was never intended to imply that the AT&SF departed Philadelphia, more that train travelers were coming west from far away places like that, and with some tweaking Warren and Mercer could make the lyric rhyme.
The Harvey House restaurants grew out of the need to feed rail passengers in the time before on board dining cars.