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And there was nothing wrong with that thought process. It is conceivable that they might have factored in something if they could predict exactly what the potential impact would be, however as you indicated no glass is optically perfect and so even within the same manufacturer there could be prevailing slight aberrations on the production line.
And the other factor is that manufacturers don't typically go with just one production run from one supplier for parts, but usually have several suppliers so that they have ample quantity available for production and potential shortages don't interrupt their manufacturing process. The same glass from three different manufacturers, (although within specs), is still going to have 3 different sets of properties. So just like no two that roll off the line in the same manufacturer are going to be atomically or optically identical, even more so no two coming from two different manufacturers are going to be optically identical either.
The Saving Grace is that the autofocus method used, by its very nature takes into account any aberrations in the lenses that may change focal length. To the autofocus system, a difference in focal length of the lens is simply interpreted it as a perceived difference in the distance of the camera from the subject, and simply corrected for by changing focal length.
What they can't account for unfortunately is out of round or astigmatic lens issues. Fortunately, those issues often can be corrected digitally through software manipulation of the images before being saved as an actual photo. Therefore as long as the lenses are ground perfectly circular, and flat glass is as flat as it can be, the focusing will simply adjust automatically for slight differences just like it adjusts automatically for differences in distance.
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