Are you gluing also? The screws are only to hold the pieces together until the glue dries, so short or long no matter. But if you use the hot melt glue like in the Project Arcade book, then that is not the case, as that type of glue is not for strength.
Pre drill the holes, and make sure the screws are not too long to go through both pieces. 3/4" plywood and a 3/4" stop = 1-1/2 ", so 2" screws would go too far through.