Conflating PN and MN is not just the sin of the ID movement. The second Truth Project video was quite guilty. They presented Carl Sagan's view of the cosmos (the cosmos is all there ever is, was, and will be) without pointing out that this was Sagan the Astronomer speaking as Sagan the (rank amateur) philosopher. Science makes no statement whatsoever about whether or not the cosmos is all there ever was, is, or will be.
I don't know if Sagan would admit that he was, at that moment, preaching philosophy and not teaching science. But the Truth Project people should have pointed all this out, if they are in fact deeply committed to the truth. As they left it, I am certain that the impression for many was that a scientist (Sagan) speaking as a scientist was claiming that science teaches there is no God.
My cynical fear is the Truth Project had no interest providing instructional clarity in this instance—that they find it advantageous to confuse philosophical and methodological naturalism, in order to further the anti-science bias that is part of the Focus on the Family world view.
Now in the video they showed another egregious example of PN/MN conflation from Cornell biologist William Provine. This charming man is a master of confusion. He writes:
Naturalistic evolution has clear consequences that Charles Darwin understood perfectly. 1) No gods worth having exist; 2) no life after death exists; 3) no ultimate foundation for ethics exists; 4) no ultimate meaning in life exists; and 5) human free will is nonexistent.
What is interesting here, and it is pure speculation, that those who agree with Provine would be strange bedfellows indeed. They would include some of the new atheist school who would like to conclude that evolution scientifically proves what Provine claims as its inescapable consequences, and those anti-Science Christians who, to vilify science, would also agree that such nonsense is the scientific consequence of evolution.