Profit or no, this movie is is still the second lowest grosser in the franchise, right above the most despised sequel perhaps on genre history (AvP:R), but cost twice as much to produce and market. I don't see Covenant being considered a flop, but there is no way this can be spun as an acceptable gross. For a franchise with 1-6 sequels planned, this was disastrous. As an experiment in trying to be more commercial, it also failed. The Alien brand has declined with every film. Only Prometheus reversed that trend. All across the board, Prometheus did better, sometimes massively so. Profit or no, this movie still underperformed all the way up to the limit of how badly it could have failed before being considered a flop. Ridley's biggest flop will always be 1492: Conquest of Paradise. But Covenant might be Scott's biggest disappointment. They were clearly hoping for a sizeable profit and sequels in order to conclude their story. I doubt Fox will have any profit from this movie in their hands by the time Scott was hoping to film Covenant 2. The best we can hope for is a cheap Ridley Scott sequel to finish the trilogy, but even that might be too much to hope for. I think any future Alien movies will be pure genre product, focusing on lots of action and horror and spending less on talent.
The real question is, once these current heads of Fox are excused, will we get a proper Prometheus 2? I think they need to distance to themselves from the Alien brand and give us Visionary Ridley, not Hired Gun Ridley. Show us a visionary sequel and all is forgiven. If The Martian proved anything, it's that a sufficiently engaging human story does not require action scenes and gore. Audiences would have seen Paradise without the recasting and revamping and reintroduction of the beast. Your story has to be everything. Covenant dropped the ball on story in a gigantic way, and it introduced a new lead who really contributed nothing to the story besides being a Ripley stand in. The third and final movie should contain all of the story left to tell - no more withholding for sequels! Give us two hours of compelling story and keep the money you would have spent on action and movie stars. Sci-fi fans are sustained by visionary images and a story that takes us to uncharted territory with mindbending obstacles, but you have to care about your characters. Killing Shaw and sidelining the new female lead shows contempt for character. Action is something you include of you have an addition to it (Cameron, Bay, Blomkamp) off studio requires it. Let Ridley off that chain. He can command audience attention with pure vision. But they also have to stop frakking up any potential to develop strong human characters. Covenant was a disaster as a story and was almost a disaster commercially. The next movie needs to have an abundance of artistic integrity and no more Alien tropes.
Adapt and evolve or perish.