"What is beautiful differs by culture" and "You are beautiful just the way you are" seem a little hard to reconcile
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No conflict at all: no matter what you look like you are beautiful just the way you are because some culture somewhere thinks so. It does sort of lessen the impact of the word, though, I admit.
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Context. One about accepting cultural diversity and the other is about accepting yourself in this diverse world. They aren't mutually exclusive. We should neither shun other peoples' perception of beauty nor shun our own beauty in it's various forms.