
I've watched Covenant twice & read the novel once. I could be wrong but here are my thoughts regarding the sequels after Covenant:
1) In Alien, the space Jockey, derelict, alien & eggs are already happened 2000 years ago or more, but the space jockey has failed to wipe-out humanity civilization
2) In Prometheus, the awaken Engineer realized they have failed.
3) What happened in Prometheus & Covenant are totally different plot/timeline that it will not connect directly to Alien movie, but related for us to understand
4) In Prometheus & Covenant are for David to learn alien pathogen & recreate his own Xeno version, that's why it's different maybe even better version
5) Engineers civilization is probably dead & human civilization is dying
6) Maybe, David will start his own, new civilization, maybe at Origae-6
7) Maybe, there will be war of Gods or Civilizations, who knows