I think they take the 1x extra of the 2 5x figures from each case and those are the ones they allocate to the sale page for the individual figures. They then keep the rest of the stock (the 4x quantity of them) available for those that order from the set of 3 web page, so they have a 4x amount for all figures available for sets of 3 orders.
That way they have enough for all the individual sets of 3 they will sell, and can sell of as many of the excess 1x individuals as they can. So when a set is ordered, it doesn't affect the excess stock of the individual figures set aside for sale. And when an individual figure is ordered, they limit the quantity on that page that is available for order so it doesn't cut into the figures from the sets. They will probably still end up with excess of the extra figures, but less than they would if they sold the 4x per case one individually and couldn't sell them all in sets because they sold out of that one.
They could set aside a small amount of the 4x per case figure for individual order, but they would just end up with more of the other figures because they would have less complete sets they could sell.
As for other retailers, most of the ones that sell individually are overpriced, I would recommend maybe watching eBay, you might be able to find a local seller offering the figure for retail or slightly above retail price.