I think the game will behave fine. The Pokemon's summary should have "???" where the Pokedex number usually is. It will get registered in your Pokedex, but you'll only see it after getting the national Pokedex. If you want to test this yourself, then you can try beating Cynthia, going to Snowpoint City, boarding the ship, getting the super rod, and catching a Clamperl on Route 219.