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I think you've gotten good answers so far. One point to make is that if you are running 2-3 camera bodies and using a certain lens on all of them then it may be impossible for Canon to properly calibrate them all together. This will really be impossible if you send 3 cameras and 3 lenses (especailly zoom lenses) and want them all to work perfectly no matter what combination of lens + body you choose when shooting. In this case they would have to involve in camera MA adjustment also because it would be like a 1% chance that...Show more →
Expanding a bit on the thoughts above, whether Canon is doing calibration adjustments or you are doing micro adjustments, getting a "perfect" adjustment requires the camera's sensor plane to be precisely parallel to and at the exact same height as the adjustment target. And, even if the adjustment is made perfectly in such a manner, that adjustment is not always going to transfer to perfect focus in real world shooting. If you are shooting a subject that is not perfectly flat, perfectly parallel to the sensor plane, and precisely at the same height as the sensor, minor focus imprecision is likely to result. Again, though, that minor imprecision is unlikely to make any meaningful difference in an actual print or in looking at the image at normal viewing size on the screen.
Many of us have learned that you can drive yourself crazy trying to get 100% consistently accurate focus. After a period of time of trying for such 100% consistency and driving myself crazy, I ultimately decided to take this approach. Unless I'm noticing consistent front or back focus in actual photos, I don't even bother trying to get "perfection". If I do notice a consistent pattern of front or back focus and if a very carefully and properly done micro adjustment test shows that there is a few points of micro adjustment called for, I will make that adjustment. On the other hand, if I see that the amount of micro adjustment called for is 10 or 15 points, my choice is to let Canon do a proper calibration, which should, again, yield more consistent results at varying distances and in varying shooting situations.
And, regardless of how much AF systems are improved and regardless of whether you are using a 20D, a 7D, a 1Ds Mark III, or a 5D Mark III, those (minor) focus inconsistencies are always going to exist because the precision of the AF system is always going to be dependent on the camera's sensor plane being perfectly parallel to the subject. When we were using 6 or 8 or 10 mega pixel cameras, focus inconsistencies were less noticeable. But, with cameras with more pixels and higher pixel density, the inconsistencies become more noticeable to us because, when we look at pictures from cameras with more pixels and higher pixel density at 100% or 200% on the screen, we are looking at a smaller portion of the complete picture and enlarging that smaller portion to a greater extent. When we do that, we are also magnifying any imperfections to a greater extent.