I would hazard a guess that the 'Engineers' on LV-223 were not direct descendants of the 'Creation Engineers' seen at the start of Prometheus but just another seeded race. That would explain their different technology (the Juggernaut vs the Flying Saucer and the biomechanical vs the simple robes) as well as their motivation (one creates the other destroys). When David is talking about the human race he means every race created by the Engineers.
Those could just be different factions of Engineers, the styles being due to different cultures.
Like how a Shaolin Monk wears robes while you likely wear something a bit more tighter.
Their different motivations are due to different agendas, one faction seeks to create while another destroys.
The Juggernaut and the Flying Saucer are basically different classes of Engineer ships built for different purposes. Like the Nostromo and the Sulaco are for humans.