No, VAT does not come on top of what you charge. Price is final and includes VAT. In fact, 16.67% of what an end user pays.
Since software production cost is rather limited, value added is a large percentage of software. hence the impact of VAT is much greater, than, say, a brick and mortar business with 15% margins.
De facto, value added tax impacts directly the markup (gross margin). So it does indeed impacts profit.
In the US, or back some 40 years ago in Europe, sales tax works like you describe. The sales tax comes on top of what you charge. Say you sell a software $100 in California, customer pays $109. It does not impact at all the gross margin.
At any rate, at the risk of repeating myself, I consider it less important to whine about VAT, than to have the best marketing, in order to offset business costs of all nature. There are considerable improvement to make right and left about software sales, would that be to be present in major online stores like the MAS and Windows Store, to make sure evaluation samples are seen and readily available, to have decent and efficient web sites, to make it easy for customers to purchase, to create new software on a regular basis, to iterate versions to cover all bases, and so on.
The app market is very competitive, but also extremely profitable. In another life, I used to sell cameras. With the best of margins at 30% and much more often 15%, not to mention inventory weight, it was no piece of cake. Software costs close to nothing to produce. Even with the 30% cut of online stores, gross margin is close to 70%. I know not many industries where it is as juicy.