Like any manufactured good there is some 'range of acceptable deviation from standard with both the camera and lens. Unless they have changed it recently Canon generally recommends that if you use the AF micro-adjustment settings your target be at a distance equal to 50x the focal length of the lens while Michael Tapes suggests that a 25x distance yields better results - but those are not for macro situations obviously. I do not know what parameters or how Canon tests the AF systems in sample lenses and camera bodies. Logically they can't test every lens and every body they make because otherwise nothing would ever be able to leave the plant as every lens would need to be tested with every body they make.
You might try placing the target close enough to fill the frame and see if that helps.
With Macro work, if at all possible I try to use Live view to focus with , using either the preview on the back of the camera or a remote live view screen / camera controller for a smart phone. tablet, or computer. for that purpose I recommend the CamRanger , http://www.camranger.com