The MTB Direct peeps got back to me, they had made some price adjustments across a bunch of products and I was unlucky with this one, so they gave me $40 store credit to bring it back to the original discount. I added a bottle of mineral oil which I'd almost forgotten, checked out and my shoes and stuff are on the way. Great customer service.
On the different prices for different styles/sizes, it seems a lot of places do it. I guess when they buy a bunch of stock and nobody likes a particular style/size they clear it out at lower prices.