It won't be split. FDS is faster than emulator for most (if not all) PS1 games. Regardless, I wouldn't recommend being hung up about 2 seconds in a 3 hour long run that has plenty of mistakes and timesave throughout. I do know my run had a strong opening, but I doubt there are many inaccuracies considering you're able to keep up in the other categories. Good luck!
After watching most of that video it just seems like you aren't as practiced in the category as I was when I did my run. You can't expect to tie a record because you copy the route. If you're looking for advice on where to improve that's one thing, but assuming there is some sort of hardware thing at play isn't the right thing to jump to. Yes, loading screens are affected (and has been known/acknowledged as a non-issue in most communities if console is faster), but nothing else seems to be. Keep practicing, and ask for help if you need it.
