I don't think it has much to do with Bush, honestly.
The reason I asked if you read the article was because the sorts of conspiracy theorists the article is describing don't usually appear to be responding to any particular presidential administration when they're spinning out their theories. "Loose Change" definitely puts forward a deranged idea about the Bush Administration. But I don't think it makes much sense to call it Bush Derangement Syndrome given that there is little if any reason to believe that the sorts of people that make these sorts of films wouldn't have made them had Al Gore been president during the attack. After all, it was argued that President Clinton was going to take everyone's guns away and throw dissenters into FEMA Camps. There are people saying the same thing about President Obama. Just look at someone like Alex Jones. He didn't start saying crazy things about the government when Bush took office and he didn't stop when he left. There's something else going on.
Furthermore, what undergirds a lot of these conspiracy theories is a belief in the New World Order or Illuminati, which as the author notes goes back to anti-Semetic propaganda of the 19th century. In that scheme, presidents and political parties function as puppets for some shadowy masters. In other words, it's crazy. But it's not necessarily partisan. Sometimes it takes on a weird religious flavor, with the Illuminati being literally Satanic and infusing popular culture with Satanic imagery. Sometimes it's more political, but even then it usually leans right in its way, with the focus being on protecting an absolutist reading of the 2nd Amendment.
I mean, there are definitely deranged and irrational responses to presidents but I don't think 9/11 trutherism really fits well with that narrative. In other words, I think this is just one more thing that Charles Krautheimer is wrong about.