Why do you presume that, Fine_Art? This is out of my area of expertise, but my general understanding is that the Phase Detection autofocus system does not measure the light at the plane of the sensor, but diverts a portion of the light which has reached the mirror, to separate AF sensors located elsewhere.
I would imagine that the precise position, orientation and distance of those AF sensors within the camera body could affect the accuracy of autofocusing. But I'm just making a reasonable assumption based on very limited knowledge of the process.
Your post was talking about lenses so I was talking about the errors in the lens. Yes, you are right the errors in the body will impact the AF as well.
I don't think displacement of the mirror, assuming it stays at 90 degrees, would have an impact. Only a offset of the portion of the image that hits the sensor. Since you see the same thing through the viewfinder you would adjust to what you want in focus. If it goes out of 90 then there would be an error + on one side of the image and - on the other. If the Af sensors are at a different distance from the sensor plane that would make an AF error.
The body seems fairly simple compared to the complexities in the lenses. The lenses change FL so errors are magnified. The mirror just changes the direction.