You seem to be implying the one-sided and derogatory use of the term "conspiracy theory." The corporate media has given this word such a negative connotation, associating the term "conspiracy theory" with irrational thinking. However, if one critically examines the official narrative of 9/11, one finds that it is itself a conspiracy theory- the official conspiracy theory, in which a bunch of radical Islamists hating America because of its "freedom and democracy" launched a highly sophisticated operation planned most likely from a highly specialized cave base.
The official conspiracy theory has been sunk under a deep sea of scrutiny for many reasons including a number of prominent contradictions, omissions and distortions- ie: not considering the totality of evidence but rather a narrow portion of it; and because the Commission that contrived this official theory was not only massively underpaid in comparison to other federal commissions, it was itself riddled with a gigantic conflict of interest- its lines of inquiry were lead by a man ideologically intimate with the Bush administration (a suspect), but it also failed to investigate the totality of evidence (which by the way, neither the general public nor relevant experts have access to the totality) and because it demonstrably began with its verdict (bin Laden did it.) Beginning with a verdict and gathering evidence for that verdict is called completing a prosecution, not an investigation.
You cite Popular Mechanics as a valid source of 'debunking' alternative 9/11 theories. Well, interestingly enough, Popular Mechanics, itself taking on a one-sided approach, has since then been debunked too. One prominent book in which Popular Mechanics is 'debunked' is Prof. David Ray Griffin's
Debunking 9/11 Debunking. Another is this article by Jim Hoffman:
http://911research.wtc7.net/essays/gopm/index.html