There are 386 pokemon in the Pokedex for Ruby/Sapphire, yet half of them had zero effect on the game. Don't use those Pokemon on trainers and don't put them in the wild. Simple as that. But if you are really hellbent against it, you can always expand the Pokedex yourself: https://www.pokecommunity.com/showthread.php?t=324892. Apparently there are aspects of that method that are broken, but I think the 650 base you're referring to is based on that tutorial anyways, so that isn't really relevant.But they will still be in the pokedex I think. Also there is no working download for the 650 patch.
What? Why does it matter? If you don't place wild pokemon & stuff beyond 493, the in game pokedex won't go past that number anyways. If you're referring to some script or routine that checks if the dex is "complete," that would be a pretty trivial fix as well. If you really want to remove them from the pokedex (and I still have no clue why you'd need to), if Emerald is anything like FireRed, there's a table that converts species index to pokedex index, so I suppose you'd modify the table to stop the new Gen V & VI pokemon from having dex numbers (think of the limbo slots between Johto and Hoenn mons).Then how are they supposed to complete the pokedex?