I wonder if it's more an indication of DSLR's pushing the envelope of what's possible optically than Canon's quality control. Dealing with such tiny sensors that are very sensitive tends to magnify the tiniest of optical errors. Optical design hasn't really kept up with Electronic design- it doesn't follow Moore's law.
Having said that I have a very hard time believing that you can adjust a zoom lens by changing the back focus distance by 5 mm or whatever. Lens focus tends to change a little when zooming and a little when stopping down the aperture. So a fixed number probably isn't always going to work.