Even better: one can ask the right people to create a "recipe" to make this work with a favorite online publication. I did so with The Online Photographer and Luminous Landscape for example.
Note: I have earlier succeeded in changing the margins and justification (from Full to Left) on my Kindle 3, but for some reason it hasn't yet worked with my Kindle 4 (compact model), even with the latest versions of calibre and KC, durn.
Update: it turns out one has to go to the Home page on the Kindle before doing the procedure, after I did that, it worked. (The author told me: Setting the margin or justification doesn't work for all books. Are you testing with the same book?
Have you definitely gone to the home page of the K4 before connecting to your PC and running the plugin?
Have you restarted the K4, not just powered it off?.)