If the actual cost of service was pro rated across apps this would basically eliminate free and low cost apps. In fact how would you price this in the first few years of the App Store when it lost money? Furthermore it would make it incredibly expensive and therefore risky to develop launch an app. They would likely have had to charge hundreds of dollars, perhaps thousands per app in the early years, stifling innovation and strangling freemium or free offerings. The App Store would be a very, very different place today.
This would be like supermarkets charging product manufacturers a uniform fixed rental for shelf space. No supermarket would stock toilet paper, it’s too bulky and low revenue, or if they did they have to charge a lot more for it.