Yeah, loading a save state is different from loading a PS save. Save states capture the state of the entire virtual machine at the moment the snapshot is taken. That includes what's in VRAM, regular RAM, caches, etc. By loading a save state with a modified disc image, you would probably get random crashes eventually, due to disagreements between the old snapshot and the new "disc". Even if you don't, the main executable will never be reloaded from disc after loading a save state, so any patches applied there would be absent. Other patches that seem to be missing might pop-in slowly, whenever the patched files need to be loaded afresh.