I got the feeling Fluttershy just doesn't care for that sort of thing as much as Rarity does. She may go to the spa more to please Rarity than to please herself. I mean, most girls like spa days, some just more than others. Fluttershy may see some of the treatments Rarity gets as unnecessary for herself. Rarity is all about fashion and looking good, while that is likely not a high priority on Fluttershy's list. And perhaps that non-necessity was what made her so popular to model anyways. Is it possible she has more natural beauty than Rarity? Perhaps. Since Fluttershy doesn't use tons of make-up and clothes to flatter herself, perhaps her true beauty shines through: herself. Some people do have natural beauty, but they don't see it in themselves. They may be more beautiful than those who do themselves up to try to impress. They are beautiful just the way they are.