What this is about is one of the biggest problems in human understanding and communication. I've said it before and I'll say it again: Almost all arguments between people are based in their speaking different languages and not knowing it, and thus working entirely in non sequitur and not even knowing it. This extends from simple differences like having been privy to different information and using different definitions of the same words to differences in the entire way they view the nature and purpose of language, not to mention truths.
Imagine, if you will, the stereotypical argument between a Hollywood atheist and his arch nemesis, the straw Fundamentalist. The latter is quoting scripture to prove his belief, which of course means nothing to the former, who is astonished that the latter even believes that what he's even constitutes an argument. It never occurs to the Hollywood atheist that when he uses an argument based on empirical observations and rational judgments, and takes apart the logical inconsistencies with the Fundamentalist's texts, that he's making the exact same mistake in assuming his obvious logic even addresses his opponent's argument.
Now, this is one extreme, using strawmen. Stuff gets real messy when you start working with real people, who work with a big mixture of axioms which exist all along the scale on a bunch of different axes, all of which constantly move around throughout shifts in persona, mood, emotion, memory, etc (a fact they're frequently unaware of), and from there take what they're working with and attempt to reach out to another person's paradigm and clumsily attempt to use it to explain their own conclusions.
This is the kind of problem we encounter in WTFDWK, and all the other instances of New Agey literature whoring out "quantum physics" as their favorite buzzphrase. You get some people with an idea which may make a lot of sense in context, and it's essentially intuitive in form; It's an understanding using parts of the mind that doesn't work with words, and is dealing with a very large and abstract pattern. Problems start to come up when they attempt to communicate this information -- first, to the rational parts of mind, and then to other people. They'll frequently try to use words, which are notoriously ill-suited for such information, but an awareness of that limitation on both the part of the transmitter and the receiver and some skillful elegance can go a long way. You work with things like poetics and various other artistic forms, or you get things like my LiveJournal entries where I give you a pile of reminders that I'm being metaphorical and indicative of a general idea then proceed with vague descriptions, obscure jargon and frustrating noncommittance.
The result is that most people's eyes glaze over and they move on without worrying about it and people with a compatible enough mindset understand to some degree what is being expressed (or a different mindset which can interpret what they're seeing into something entirely different, something which makes sense to them, which is also valid as long as everyone stays aware of the inevitable distance between what their reality and other peoples'), which usually won't be too new of information to them (at least on the intuitive level) but it can help them consider possible adjustments, see how what they already know could possibly be expressed, and most importantly, remind them that they're not the only freak who thinks like that. That last bit is invaluable, because people with that sort of intuitive/artistic mindset are often starved for encouragement for a lack of ability to communicate what most of their life is really like, and their occasional forays into expression tend to be met with a lot of dismissal and occasional high points of incredibly hostile reaction -- heckling the weirdo, medicating and heckling the child, institutionalizing, medicating and heckling the delusional, and lynching the fag.
Then you have stuff like our movie here, where they try to take what they figured out with an intuitive mindset, try to reduce it to something they can express, and then attempt to reach out and explain it using the words more scientific paradigms, which they don't have a very strong grasp of. This will have the same result of connecting to people who watch it and understand the intuitive level of the message, and either don't know enough to dismiss the pseudoscience or understand that it's not actually about the pseudoscience. Meanwhile, the people who view it rationally, trying to follow it from evidence-to-conclusion will see nothing but nonsense and will be even more steamed to dismiss the conclusion if they ever see it anywhere else, even if it doesn't use pseudoscientific context. And of course, you have people like the interviewees, who were terribly offended when the creators took what they said, cut it up and rearranged it into something different to fit the conclusion they had already started out with.
They didn't have to do that, though. Taking a conclusion and rudely rearranging information to fit into it isn't the only way to form a top-down explanation of reality. People are learning to pay attention to the deeper, more abstract essences of their faiths, and see how they can reconcile them with the currents of science. Worldly details of physics, biology and psychology are seen as the means through which higher principles manifest, without being dismissed as incomprehensible or as an intentionally deceitful illusion. Most Christians these days don't believe the world was created in 4004 B.C., or that Hell is a fiery cave full of Doom monsters. (For that matter, most of the ancient Greeks didn't believe that lightning bolts came from a bearded dude on top of a mountain; The rap we got in elementary school about how ancient myths were supposed to be direct explanations for things people didn't know is a diaper full. Despite being currently unfalsifiable, not many people actually believe we're all wired into a robotic power-grid in a post-apocalyptic future with Neo flying around trying to save us, but The Matrix is still a very relevant illustration of some otherwise really heavy philosophical concepts.)
Of course, it is entirely possible that the creators of WTFDWK knew exactly how bogus the pseudoscience was and went through with it anyway. No, not just to make money or raise a cult... The pseudoscientific format they used just happens to be the form of artistic expression many people are most receptive to! This is why you have people claiming to be abducted by aliens in a spaceship from another planet, but wouldn't consider saying they had an encounter with spirits or fairies or angels or whatever.