I just realised something, is it just me or is pipp the only multicoloured pony ever shown in the show.
Haha. That's a good observation but Luna out of the four princesses seems to have the strongest bond with children as she protects and guides them in their dreams and she's part of a fun holiday for them to engage in.
The disorder is called vitiligo, and it causes the skin to become splotchy.
Ponies seem to universally have single-colored coats, except for pip, so it's not hard to imagine that it's done sort of equine vitiligo. After years of feeling isolated in his own skin, it would have felt very good to not only find someone like him, but a princess no less. Luna chooses not to tell him the dark patch on her rear is part of his cutie mark because she wants him to feel like he's not alone.