The difference now is the developer no longer has a developer's license. The cost of the store is not distributed over the number of stores you sell. The developer has to compete with the $200 solution with no advantage. This takes $200 right off the top. As someone else pointed out, before you could offer a slightly customized PS for the same price as the off-the-self version and still make a profit.
Since the developer now is in direct competition with the publisher of the tools, the only way to differentiate our sites is to use other tools that are not in PS. The publisher will always have an advantage since they can sell as many copies as they want for pure profit (after development costs are covered). We, on the other hand have to pay $200 a copy.
This will not effect larger projects that require more than what PS offers, but it takes away the low hanging fruit that many that are just getting started depend on.