That's not what the numbers mean. The numbers are "owned species"/"seen species". Both values are those from the National Dex (i.e. all Pokémon).
It's easy to change these values to a Regional Dex's values, so long as you only ever want to use one Dex's values. At the top of PokemonSave is the code which sets the displayed information, and it includes the phrase $Trainer.pokedexOwned,$Trainer.pokedexSeen. Change this to $Trainer.pokedexOwned(0),$Trainer.pokedexSeen(0) to use values from the first Regional Dex, or use 1 for the second Regional Dex, etc.
You'll need to do something similar in the PokemonLoad script section too (line 346).
It would be more difficult if you wanted to vary which Regional Dex to take the values from during the game, mainly because the load screen only has a limited amount of information available to use.
If your intention is to make a game with just a limited Pokédex (i.e. create a Regional Dex and call it "the Pokédex", and never access the National Dex), which is easier than cutting species out of pokemon.txt and renaming sprites/icons/cries/footprints, then you can just ignore this "problem". The Dex length is never shown, so the player will never notice that your game has more defined species than appear in it.