Liveview using live AF has no physical link to the AF points, it uses the sensor. Liveview using Quick AF does use the AF sensor, but those points are electronically generated, and there is no physical connection or link to the AF sensor or the transmissive LCD. Getting all three lined up does involve tolerances.
Presumably, the electronically generated AF point array shown on the main LCD during Live View Quick AF is 'ideal' – the center point is dead center on the image. But the AF array on the transmissive LCD should be similarly centered, as should the actual AF sensor.
That's three separate components, each of which must be properly aligned, and as you state they each have a manufacturing tolerance. It would certainly be possible for two of the three to match and the third to be differently aligned. Misalignment between the VF transmissive LCD and the 'ideal' display on the main LCD is easiest to detect (as in the OP's case), but if those two are aligned, the actual AF sensor could still be off...and that's more difficult to detect. I have carefully tested my 1D X (specifically, I tested that the transmissive LCD was aligned with the actual AF points, in Live View I use contrast-detect AF – but the transmissive LCD also aligns with the 'ideal' main LCD).