I disagree. I'm not sure how Empire and Karaz Ankor measure against each other (though Mathilde has made oaths to the Empire, and currently is not a servant of Karaz Ankor, and she seems to respect her oaths), but I would put Waystone project way below both, because it's not a certainty that it will actually help the humanity in any way. It's just one project. I think she would sacrifice it in a blink if it was a choice between the project on one side and humanity, the Empire, or Karaz Ankor on the other.
How is this not a certainty? This is literally a means to keep demons from devouring the world.
As for the Karaz Ankor part:
Karaz Ankor, Advanced: You're more at home in the Karaz Ankor than the Empire you theoretically owe allegiance to. +2 Diplomacy