Hey there @ajlino ,
I am in the same boat as you with this issue. I have a 2 player cocktail table built running Retropie on a Rasp Pi 3.
I understand that not many roms support cocktail mode where the screen flips for P2, but I was hoping at least games like Pacman, DK, Galaga would work since the versions of roms I have appear to support this. But for the life of me I cannot get this screen flip to work at all on any game. I did manage to get Galaga to flip for P2 but it was all messed up and not playable.
Did you ever have any success on getting this screen flip in 2p mode to work? It's frustrating seeing videos online of people getting this to work with no issue at all, and I am following the same exact method.