I suppose it depends on whether you agree with standard prices, or not. In many markets, resellers, retailers and other sellers are free to set their own prices for a given manufacturers range of products.
At the end of the day, any company using PPC to promote their own products has another huge advantage over their affiliates... they can afford to bid more because of the higher profit margins they have.
I mention this to just try and make the point that there are various ways in which merchants can outgun their affiliates. It often comes down to whether a company decides to actively compete against affiliates, rather than how they do it.
The price difference is just more transparent.
Perhaps they see Adwords and Clickbank as two very different marketing channels - tending not to overlap much.
Just a thought,