Kkat never gave a description of Littlepip's palette. She actually said the following: "I've intentionally never mentioned Littlepip's palette so that it was up to the readers how they envisioned her, much like you can choose your own character's design in Fallout. I felt that this freedom of imagination would be a nice touch considering the first-person perspective."
The grey or grey-blue Littlepip basically follows from the colors the first person who drew her chose.
Personally, I prefer the grey version over the other colors. I'm not so fond the the blue-grey version. Like you I could have started with Rarity - I actually bought one, but doing Littlepip in this color appealed to me, I guess for artistic reasons, and because she wasn't grey.