Hoenn Dex Order is the one that controls the Hoenn Dex list in the Pokedex (maybe that your problem with the "I saw wurmple, poocheyena, zigzagoon and torchic, but my seen flags register vileplume, ninetales, gloom and raichu. If I see one more pokemon, deoxys gets registered."). Without that, you cannot set expandables in the Hoenn Dex. It is just in case you want to customize your Hoenn Dex.
Animation Timing 2... I can't get about it but someone recommended to expand it also as well. A post at the near end of the thread which is about expanding animations.