@JBroida
Please take another look, This time focus not on the lines straightness, but how low it is from the edge to the line on the left, and how much higher it is on the right. I have not seen anything ever close to that except perhaps an early Davou.
If it bothers you, return it and ask if they have a different one, although you may have to pay a fee. The fact that the shinogi isn't parallel to the edge means that either:
1) the sharpening angle of the blade road is bigger near the heel than at the tip, or
2) the blade is thinner above the shinogi near the heel than it is above the shinogi at the tip.
It won't be a problem in use or in sharpening, but if the aesthetics really bother you, send it back. It's not going to be easy to straighten it out and have it look perfect.
Edit: err, I guess I should be responding to
@matc. Also, maybe I should say that in general, wobbles or "imperfections" in a shinogi line are more likely to be due to variation in the geometry of the knife above the shinogi than below the shinogi.