I think they're valid in calling the deal "secret," as the app-buying public at large has no idea these deals are taking place. The developer knows they're getting nothing, but everyone downloading the free app is harboring illusions that they're supporting the developer.
Maybe not everyone, but certainly a non-zero number of people. As I read this I started feeling bad for the daily free apps I've picked up from Amazon thinking the developers were getting paid. At least now that I know I can go actually put money in their pockets. Hopefully others feel the same way.
I had no idea 20% was expected to be paid to the dev and I've downloaded several from the Amazon App Store. It sounds like this dev made an uneducated choice to be featured even after knowing they would receive zero %.
At the very least you have to say their choice was educated - there was a debate, they decided to go ahead and do it, it didn't work out, they're shifting their resources as a result.