I don't know enough about SNES hardware or the level of in system debug, but could one generate a hardware test jig that was able to record player traces that could be re-run in the emulator and have the screen grabs compared? Given the system state, random number generator and the series of up/down/a/b one should be able to recreate the same game evolution and video output from the emulator?

Then you can form a reference set of captures, real hardware and the emulator. Screen to screen emulation with diffs could then be an accurate tool to measure against actual hardware and the accuracy gap between the two. No? Controlling the random number generator sounds like it might be key. And some player traces might be really fragile in the input timing search space.