I don't see how species sharing features like complex organ systems casts doubt on the idea of speciation from common ancestors. If anything, that is support for the idea.
For the second part, an organism doesn't need to know why it's doing something in order for the thing it's doing to be advantageous. Inherited "knowledge" is really just inherited behavior.
For the bird example, that's brood parasitism. Cowbirds are a good example. The only two behaviors you need for it to work are 1) the adult female needs to lay her eggs in nests that are already constructed, as opposed to building her own. Nothing too complicated there. That just saves time and energy. Importantly, since none of the females of her species build their own nests, there is zero chance she will accidentally lay eggs in a nest of another brown cowbirds. There are no cowbird nests. The second thing you need is for the offspring to be aggressive towards its nest mates. Again, there's an obvious advantage to that behavior in that, without competition, that nestling gets more food.
There's no need for the mother to "know" why she's doing what she's doing, or to pass along the knowledge of what appears to be a complex strategy to her offspring. She just has to be too lazy to build a nest and the offspring just has to be hostile to other chicks. Voila, you've got brood parasitism.