Not a nutritionist, but I believe the answer falls into two broad categories.
One, chemical: processed foods frequently contain additives, e.g. preservatives, that less-processed food doesn't.
Two, physical: a peach smoothie is digested and hits your bloodstream differently from a whole peach. They're chemically identical but physically different, and that changes everything from how quickly you ingest it, how much of it you ingest, how it hits the stomach and how it hits your gut.