To be fair, there is still room for the space jockey to be a separate species. the details, size and proportions are different from the pilot Engineer. The Engineers are also genetically human, so not the creators as they evolved on earth. Much like Prometheus, they likely stole the fire from the gods (Space Jockeys) after the gods uplifted some early humans to serve them. The Engineers are adapted to life in space but are human. The creation scene at the beginning was obviously not humans being created but the Engineers creating (or attempting to create) advanced life elsewhere.
The Deacon Alien was already seen in the murals in Prometheus, as were Xenomorph hands and eggs as well as facehuggers, so those obviously pre-existed, so David did not create the Xeno's. He just simply created his own version using the goo.
Also, the ampule goo containers had a couple sizes and different words written on them, so there is likely more than one kind of goo, each of which does something different. When they all leaked onto the ground and mixed up the effects became unpredictable. The one David took was small and obviously designed to spawn (after a couple stages) the Deacon.
