You guys know Bethesda owns Arkane, so they can make them do whatever they want them to do. During production of Dishonored, Bethesda started to arbitrarily reject milestones. In doing so, the then-independent-Arkane had to find ways to pay their staff since successful milestones are what feeds the bank. Knowing that Arkane wasn't making their milestones on time and potentially going to suffer internally, such as loosing staff, or ultimately shutting down, Bethesda's parent company Zenimax stepped in to help Arkane out by floating them loans during this "quality issue" period. That seemed nice of Zenimax to help out Arkane, right?
Now since Bethesda had been rejecting milestones because they didn't believe Arkane was maintaining the quality they originally promised, Arkane's also severely behind schedule because time has been spent correctly and addressing Bethesda's issues with previously rejected milestones.
Since Zenimax is also the company that's invested in Bethesda, they start telling Arkane they have serious concerns about their ability to finish the Dishonored. Even though they originally floating them loans to keep Arkane running, they now give them an ultimatum: pay back the loans or sell them the studio for some piddly amount. If Arkane doesn't do either, then Zenimax will take them court for breach of contract since they're now so far behind in the project.
Remember, it's because Zenimax's company Bethesda has been rejecting milestones that put Arkane behind in the first place.
The outcome is Arkane reluctantly sold their independence to Zenimax so they could continue the creative work they started and at the very least have public recognition for their efforts.
This is why Bethesda can tell Arkane to do whatever they want them to do now.
What would you do if you were making Prey 2 and started wondering why Bethesda was suddenly treating you differently? You'd start looking at past independent developers Bethesda has had deals with to understand if it's a developer issue or a publisher issue. When you discover Bethesda started to reject milestones at not only Arkane, but Splash Damage and inXile, you start to see a pattern. Knowing the fate of Arkane, if you were the Prey 2 developer would just sit there and see what happens or would you confront the publisher?