u/ANeomorph

So the USCSS Covenant intercepted Shaw's transmission (sent by their Juggernaut), which means that human ships can read Engineer transmissions. In Alien: Covenant - Advent (and some other short clips) we see that after David took control of the Covenant, he sent transmissions to Weyland-Yutani explaining to them what he did on Planet 4 and what he is preparing to do to the people inside the Covenant, which means that he didn't really "defect" from the company or anything like that.

In Alien: Covenant - The Secrets of David's Lab, David at the end of the transmission says "If you do this, there is no turning back. My creatures should be some clues to rule this galaxy" (or something like that, it's not very clear). Which means he is willing to let the company use his creatures.

So my idea is that David contacted the company while he was in the Juggernaut en route to Planet 4 (when Shaw wouldn't know, perhaps after he put her in hypersleep in Alien: Covenant - Prologue: The Crossing) - perhaps telling them about the Engineers and what happened to the Prometheus mission. The company then instructed him to release the Black Goo upon reaching Planet 4 in order to kill the Engineers there. Why? Because the Prometheus' crew encounter on LV-223 made it clear that the Engineers intended to wipe out Earth (if not all of humanity across space) something the company obviously wouldn't want. Humanity stood no chance of fighting back against the Engineers, so the Black Goo was their best shot.

Daniels also said that Planet 4 didn’t show up in their pre-mission surveys and "appeared out of nowhere", which could mean that the company knew about the planet and deliberately concealed it. To take it even further, David may have somehow known that the Covenant was coming, so he somehow triggered the neutrino burst (or what the crew interpreted as such) using Engineer technology, and then sent Shaw's transmission to lure them to the planet. Also, Mother welcomed David when he took control of the Covenant, which could mean that it was all planned. The company deliberately sent a fresh ship with 2k people in that region, so that David could continue his work.