Basically, the Mulliken populations are related to the basis set, while the analysis in the paper goes more to the real-space density. Although there is naturally a correlation, precisely which charge you choose to assign to an atomic site is always a bit arbitrary (and, if you wish, not even physical, just numerical). In the paper they have a particular way of saying how much charge belongs to each atom (they take as the separation point the minimum of the charge on the bond-line), which certainly is not how the Mulliken populations are defined. So some difference should be expected.
Thus the Mulliken populations are a rather blunt instrument. If you really want to compare to the experimental results, I suggest you try to make similar contour plots as in Figs 2 and 3 in the article, of the electron density. Although VNL will not give you exactly such contour, but rather a bit more colorful ones, one should be able to compare the pictures, and hopefully find some agreement. In principle you could also try to reproduce Fig 4 but it's a bit trickier.