Exactly, the only problem is the only way to obtain them is through evolution, breeding, the givepokemon command. Any other way and the game will crash due to them not having Pokédex entries.
By the way, there is a way to expand the number of Pokémon. Jambo51 is doing it on 649 base. However it requires a lot of knowledge and experience, deffinately not for a beginnier or even intermediete. I haven't even attempted it yet because it is so intimidating.