1 - as there is no clear date on any of this it leads to assumptions. When did Sony total the sales as passing 1M vs preparing the release and getting it out? How does this correlate with VGChartz sales tracking?
2 - as ever VGChartz needs to stand by its numbers (sure adjustments here and there) otherwise it is simply providing a summary of other numbers after they are released - the old it should change to match NPD, etc.
In my experience (from retail) all numbers are subject to lag. We simply don't know which sources and when let Sony know KZ2 had passed 1M at retail. Nor how long Sony took to get the release out. Your post assumes retailers updated Sony a few days before the post based on the very latest sales. That is unlikely.
PS - I don't care either way so this isn't defense, but there are too many uncertainties to take this any other way that knowing Sony are happy that KZ2 passed 1M at retail but we don't know when it passed 1M at retail.
Remember Sony knows what it sold to retailers, but will only get partial feedback (and delayed at that) as to retail sales of the game themselves.
Try to be reasonable... its easier than you think...
