They wouldn't be solved because the problem is that newer versions of shared libraries are not compatible with older applications. There is no problem with ELF or PE formats - ELF is supported on Linux natively, and PE is supported using Wine.
APE format doesn't solve the problem with shared libraries changing over time, it dosn't solve the problem that different plaforms provide different APIs (for example, windowing APIs, audio APIs etc).
Can you see how the problem that you described in the subsequent paragraph could easily be solved if the applications were compiled in such a format?