This isn't helpful in any way though. All it would say is that for some millions of instructions, there is some inconsistency at that exact point.
We can already see these states when doing console verification. If it plays one way, it will almost certainly play in the other unless other bugs are found. (An example: SMB3 is not emulated well enough. Whether recorded on console or via the emulator, the runs will cross-sync. The bones/wrenches are the only thing I have found that does not sync up. Any interaction with these may cause a desync.)
What you are basically saying is "copy the input." The input bot would see what the output bot puts out. It would be 100% identical in all cases, without exception. I can already copy a file on a computer, but this would be a pointless task in this case.
This really makes no sense. Maybe you lack understanding of how input works on NES/SNES? If so then as I've explained, this probably doesn't work the way you think it does. If not then I call BS.