I think that they will let Scott do another as long as HE WANTS to do it...
You have to figure that FOX can always go with a soft reboot should the dredges get dug too deep.
As of now an 80million$ sequel to Covenant or even a 90million$ one, is guaranteed to at least turn some profit without hurting FOX's ability to do that soft reboot at any-time thereafter. So there really is no reason not to let Scott do what he wants within the confines of a slightly smaller budget. If we're considering the idea that people perceive Scott's prequels to have hurt the legacy, that reputation only stands to worsen over-time, for Fox, if he doesn't do another and finish the story. Imagine if Lucas stopped at Episode 2... COVENANT isn't nearly that bad.
As for the above suggestion of Ripley vrs David, well if they made Blomkamps film and brought David into that storyline as the main antagonist vrs Ripley, Newt and Hicks, I think fans would be far more accepting of a lot of things. Even if I still dislike the idea of these films retconning A3, if we get some grand-scale payoff like this, I'd be more excited about it.