I had exactly the same problem and it was real. After three service visits they exchanged the mirror box. Atfer that repair the AF points' misplacement was corrected however since then I struggle with AF system. Since almost a year from purchase the camera is being serviced all the time without any good solution. My guaranty is almost over and the camera is like piece of crap. I can only suggest you to push the store to exchange it as probably any service will not fix that. I checked 3 canon services and every time if one thing was corrected the other one was not working properly. Right now center and left points are backfocusing and right points are focusing in opposite direction. One year of frustration without taking photos. Unfortunately IMHO if you think your AF points are misplaced-you are probably right. In my camera when I focused on the edge of any target it focused far away. And it was obvious that it happened only in one edge of focus point. It is normal that the real focus point has more area than its layout in viewfinder however not only in one direction. As I said-they fix this but camera probably lost all factory tolerances and now AF is just useless.
Sounds scary. I guess I'll have to discuss the issue once again with the service. They suggested that they'd move the viewfinder inside the body so that the points get aligned. To me this sounds like fixing a problem with another one and most likely doing more damage than anything else. If they mess up the AF, a serious problem is created to replace the possibly cosmetic one.
Now that I checked the issue again, I can also see (with the grid on) that the grid lines are longer on the right than on the left side of the frame. This tells me that the viewfinder might actually be in place but the indicated points are off center. ... Well, I don't know. I use cameras to take photos. Someone else can repair these things, but I hope that the someone also knows what he/she is doing while at it.