They're using よう as different parts of speech. So the usage is different and the meaning is slightly different in each one.
1. being used as a na-adj as the predicate of the sentence (X is Y where Y is the na-adj here). It simply says "The girl's cheeks are like an apple."
2. being used as a na-adj to modify a noun, in this case 色. Swapping things around a bit to put it into decent English, we get "the color of the girl's cheeks is like an apple." A more literal translation that may show the use a bit better (but isn't very good English) might be "the little girl's checks are making an apple-like color."
3. here it's being used as an adverb to modify 赤い. So, "the girl's cheeks are red like an apple."
Manager of Mobile & Mac Applications