All applications written for the iPad (every version ever made) are designed for 1024x768 only. There are NO apps that are designed for 2048x1536. It is currently impossible because the iOS SDK doesn't allow it. Now you are asking how do retina apps work. Easy. The developer provides two sets of graphics (hence the average app size growing by 16%). One set for 1024x768 and a second set at 2048x1536. They do that by providing a graphic asset with two different names. So pumpkin.png is the 1024x768 version and firstname.lastname@example.org is the 2048x1536. The developer doesn't have to change a single line of code to make this work. He simply calls for the asset pumpkin and iOS looks at which device it is running on to pick the graphic. And yes this applies to all iOS devices.
Now with that in mind, why do they want more CPU and GPU power? There in-lies the rub and what you are concerned with. The amount of AI (artificial intelligence) and how many different 3D objects built with multiple polygons that are independently textured is limited strictly by the amount of time between each screen refresh. The more horsepower the more you can do.
In that regard, they have to code for the iPad 2 and Mini which are both A5 CPUs. That means anything they can run, the iPad 3's A5X and iPad's 4 A6X can run without any issue. Heck for that matter, the iPhone 4S and 5 are compatible with that design criteria.
Hope that elevates some of your worries.