The train and the car are transports into other places. In this case a twilight zone, the spiritworld, a japanese shadow society. The train symbolism at the end is similar as I have in dreams, and in real life when I am journeying... capturing the atmosphere of being "in transit". You'll also find trains in other metarealist works.
Perhaps the food in the abandoned town is a symbol for offerings from humans to their spirits/gods and the parents have violated this sacred tradition by not seeing that this food has a higher, or other purpose then just satisfying their own needs and so as a punishment are turned into pigs? Perhaps it's no coincidence that the girl doesn't do so as she sees more things then here parents who seem blinded, not thinking about where they could be.
Also see this site:
"Being an Inquiry into the Similarity of Story between Alice in Wonderland, The Wizard of Oz, Labyrinth... and other movies, myths, fairy tales, and fictions
Wherein a girl finds herself in an otherworldly place, far from home, where she is surrounded by strange creatures - some helpful and others very dangerous indeed - and must navigate her way past obstacles in time to defeat her adversary and reach her goal, gaining wisdom, power and sometimes even love along the way."
Note that in literature you also find a similar theme with little boys (Nils Holgerson, Neverending Story, Charlie and the Chocolate Factory), a theme of children making sense/seeing beyond/below the world of grown ups? Girls seem more innocent then boys, or perhaps the male/female aspects are of importance in these modern day fairy tales.
Another great anime by the same director, which also has something to do with the topics discussed here: Mononoke-hime. About the spirits that have poisened (our) nature, one my favorites.
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