During the time of the cutie pox epidemic, a school of thought rises up dedicated to removing the excess cutie marks. Although the small group doesn't know what started the epidemic, they try to find ways to remove them, eventually succeeding. However, that sect didn't die out when the cutie pox did. They kept the secrets of removing cutie marks, surviving in what would become the Equestrian desert.
Huh... I never thought of that connection between the cutie pox and the equalization spell. Congrats, this idea is now the part of the ammo for my head canon.
Well done for writing this story and a good explanation for the equalization spell.
6947732 Thanks!