The pokemon's gender, species, and DW move are all still generated by the online RNG (as it would be normally) and the pokemon you pick up on your game is still generated purely by the normal game mechanics (unaided) so yes, they are completely legal. All that program does is bypass the 10 step limit on the Island of Dreams (thus getting EVERY item and befriending every pokemon you could have encountered that run) as well as sparing you from playing the monotonous mini-games hundreds of times over.