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I have seen several posts claiming that switching to an AMD GPU would eliminate backwards compatibility, but I don't see why this would be the case for well engineered software ...

For the most part, game engines will perform calls to the GPU through a standard graphics API that acts as a hardware abstraction layer; and in the case of Sony and Nintendo this API will most likely be OpenGL. All special features of the graphics cards are accessed through extensions to the standard API. Any distinct features of the PS3 GPU could easily be emulated on the driver of an AMD GPU by using a similar feature on that GPU or on the CPU.

This is the reason why OpenGL was invented, and is the reason why all of your games work on your PC when you decide to upgrade your graphics card.