Until the fortunate day something definitively says otherwise, by "perfecting" the Pathogen, "David" created the Alien. As for any differences between the Alien in Covenant and the Aliens featured in the first three films, it's so easily reconcilable, from Alien The RPG's idea of three types of Egg and Facehugger and so on Praetomorph/Stalker, Soldier/Sentry (Praetorian Guard/Praetorian Charger), Queen/Empress. To the idea it's a prototype. To the idea simply all Aliens share it's features retroactively.