Yeah i agree with it being most likely a "we made more than we thought would sell, so let's allow these other places to sell it as well".
If this figure had came out years ago back when there was the huge "Brony Boom", it would have sold out pretty fast. But nowadays, unless it's something custom made or a SDCC exclusive, I can't imagine too many people willing to shell out so much on a figure like that.
That is a real bummer for the people who payed the $100+ for it on their site, since other places are selling it cheaper.