I think after Google rolled out the BigDaddy, a lot of web pages ended up in their supplemental index. They claimed that because these pages seem "spammy", because of links to and from these pages. A lot of complaints about good pages got demoted to this supplemental index. The pages in supplemental index seem to have lower chances of getting listed.
That article has a lot of misinformation in it. You probably should skip that article. (I'm a big fan of SitePoint so if I'm saying that you know that article must be bad).