I've been thinking about this for a bit. Maybe Basic Fun didn't include Spike in the RaMC set even though he's featured on the box art to make people more apt to buy the blind boxes trying to get Spike.
I just realized that set includes 2 unicorns, 2 pegasus and 2 Earth ponies. Moodancer was one of the ponies transformed by Tirac so I don't mind her being in there. Maybe BF thought the set would be more balanced with 2 of each kind of pony?
Also, I just saw that Moondancer is included in the box set and the blind boxes. I agree that is a little odd to repeat a pony in a box set and a blind box especially if the idea is to get all of the characters.
Ponyfan