I have discussed this before recently and started to in Totally premature Alien Covenant theory
I think that we would have to be shown somewhat what becomes of Shaw from when she and David left LV-223 in the year 2094 and the time the Covenant arrives on the World they find David after the year 2104......
Shaw is in the movie, she will play a smaller role... the Synopsis omits her.... yet she will be a part of the Movie..... There is in the Synopsis a Gap Between how does David manage to Pilot the Juggernaught without Shaws help, and what happens between leaving LV-223 and getting to the Place the Covenant finds David alone some 10 years after.... nevermind the premise that the sequel was always set up to explore... that is what became of the Engineers, why did they create us and why then did they want to destroy us and why and how with that Evil Biology that they was working on LV-223 with.
The only logically answer is that Covenant will in most part focus on events post David arriving at Paradise (or where ever the Covenant find him) the main Plot will be set 10 years after David and Shaw left LV-223 (if Shaw left with David?) or even was onboard the Juggernaught when he arrived at the destination that the Covenant crew find him...
But Shaw will feature.. this would either be a small scene, set prior to the Covenants arrival or after...... and regardless i dont think Ridley and Fox will throw away Shaw as there was some interesting dynamic between her and David and a interesting set of scenes to explore the relationship because without Shaw we have to assume David is going no where.... will they pass this by?
I doubt it... i think this would be explored in the next movie after Covenant, and remember the reason Shaw wanted to get to Paradise... are they going to drop the Engineers and all those questions? I hope not and i doubt it...
I think its a simple case of Covenant will be set after 2104 but we would get some scenes, that are set before this, and even thousands of years before it... but these will be a small part and parts that would be explored in depth in the next movie thus Alien: Covenant is set mainly after the events of the next movie and 3rd in this new Franchise (2nd Alien Prequel).
Reason is to cover this aspect first so that Alien 5 can go ahead without stepping on the toes and spoiling what Ridley has instore as far as Engineers and their Tech etc.