It may look as though Madame Pholnaset is able to cast an aesthetic glamour on her chocobo but it's actually an elaborate illusion. Once she looses contact with her chocobo the illusion is usually released and her chocobo's natural appearance returns.
This is due in part to Madame Pholnaset's self-centered nature. She's good (though not as good as Jandelaine de Dzemael) at performing aesthetician work on herself but not other people. She is however a very accomplished illusionist so she's able to cast an illusion on her chocobo, which isn't nearly as taxing as literally altering the appearance and composition of something or someone.
There are limits and parameters though. The further away the object the harder it is to maintain the illusion, so Madame Pholnaset usually releases the mirage once the ride is over and her pompous entrance has been made. This is especially so if the illusion is very complex.