There’s a suggestion (posted on Alien-Covenant.com) that some higher power has seeded humans, Engineers, and 3-4 other iterations of humanoids throughout many universes.
These higher beings supposedly have God-like powers, including the power to elicit massive scale natural disasters in order to change and reset ecosystems.
The sequel to Covenant is already written, so it’s likely that this core question will straddle the two movies.
If these higher beings exist, however, they could have created the xenomorph as a form of divine justice.