Given one can just reset for whatever setup is optimal (normally Exodia, or whatever is left if you ban that), it's extremely hard to argue for any form of separation. What's so much better about resetting for Cyber-Stein OTK on Joey single duel? At least with a game like FM or Sacred Cards, the run isn't laughably short and even if there are issues with separation with those games there's some actual difference.

But you can use RNG manipulation in no Exodia too. The game is so short and simple that there's really no way around that.

At some point before you go into a duel the game uses the computer time to initialise the RNG, so it determines the way the deck is shuffled. So either set your computer time to something favourable before the run, or work out what times are favourable and go for those (and they happen often enough in the day that this is completely feasible). That bit of information is the key to the entire manip and with a little bit of playing around and experimentation you should be able to figure out the rest. It's been two years so I've forgotten the fine details, but I remember it being very simple.

Depends on what you mean by 'start the manip'. You put the computer clock back a few seconds and start the run at such a time that the moment the game looks at the clock aligns with it being the time you want. I can't remember the exact moment the game polls the clock I'm afraid, all I recall is it is at some point after you click on the button to start the run.