Prey does a similar thing with Typhon powers and the ending. It seems to be a pattern with Arkane.
Uh, no, the ending to Prey and its relation to the game mechanics have nothing to do with what happens in Dishonored.
Acquiring and using typhon powers does not affect the ending other than having a line from one of the operators mentioning it in passing. That is all.
There's only one factor that affects the meat of Prey's ending :
did you try to save humans or not
Every event related to saving people, killing people, or not caring and letting them die from other reasons will be judged by the operators and the game keeps an internal empathy score about you.
If your empathy score was average or high, you are allowed to make another choice right at the end :
side with humanity
or murder their remnants and rebel (taking the opportunity when your leash is removed)
If your empathy score was low, you are executed and deemed a failed project. They restart the project with another typhon.
From a gameplay perspective, there is no dissonance. In fact, there are cases in which using typhon power will make it far easier to save lives if you're going for that high empathy score. Acquiring and using typhon neuromods is not a detriment to getting a "good" ending.