The Covenant might have left earth much longer than 10 years ago. The events of Prometheus wouldn't necessarily have had any influence on the colony ship's date of departure. Perhaps they stumbled upon the planet or David radioed them an invite when he saw they were in the vicinity.
Well it's probably just a Yutani ship init?
I really hope the Yutani and Weyland merger doesn't have anything to do with the Alien. Its just unnecessary and convenient to tie things together so much. I hate when they do crap like that in prequels.
Whilst I see your point, I don't agree with this case. Fire and Stone was edited heavily so as to not conflict with whatever the plans were for Prometheus 2 at the time. Likewise Lebbon had to edit his completed manuscript for Predator Incursion following the Alien 5 announcement. For the time being anyway, Fox seem to be going to a concerted effort with this rebooted canon, and the new novels are a big part of that.
Having said all that, Ridley Scott has always been his own man and I wouldn't put it past him to disregard anything he doesn't like.
I understand why you say what you are saying here, but I think you are reading too much into Fox's motives for making the writers of FIRE AND STONE stay away from any content that would conflict with the Prometheus sequel. It doesn't mean they want the F&S story to remain canonical, per se. It simply means that they don't want any aspects of the P2 script revealed in the comics, ahead of time. It also further reinforces them from legal and payroll disputes over the ideas presented, should different writers come up with the same ideas twice.
The fact that Fox made the writers of the comics change things, so as not to give away aspects of Prometheus 2, doesn't mean they did so so they can keep the EU canonical. I'm sure, in their minds that may be an added bonus, especially and only if fans respond well to the EU materials in question, but the de-facto reason is just a formality. They don't want things, they want the film to reveal, to be revealed before hand. Its really that simple and it is completely driven by the fact that the financial root is still, and is always, the films dictating what is canonical, without complicated cross pollination.
The exception here may be Alien Isolation, but I would almost guarantee that the exception proves the rule in this case, because I wouldn't put it passed FOX to consider adapting that game into a film someday, but only based on how well received it was. In contrast, I'm pretty certain we wont see or hear any mention of a Colonial Marines adaptation based on how poorly that game was received. Heh.
LSS The films are the raw material. Everything else, from the studio's perspective is cross-pollination and is, for better or worse, secondary.