This article about a "weird fourth dimension" that's "like time but not time" certainly seems like horse shit to me.
Using a configuration space that is a good fit for a specific system is not unusual in math or physics. It's the same thing that astrophysicists do when they work in orbital elements, or that engineers and programmers do when they make calculations in Fourier space. It's worth understanding these concepts even if you're not a physicist.
Configuration spaces are so fundamental and useful that they are introduced in the very first lecture on classical mechanics in Leornard Susskind's excellent series of Stanford physics courses: http://theoreticalminimum.com/courses
(Neal Stephenson's novel Anathem also has a simple introduction to configuration spaces in an appendix, because that's the sort of thing that ends up in a Neal Stephenson novel.)
In fact, coordinate transformations are at the heart of the modern conception of classical mechanics: http://en.wikipedia.org/wiki/Lagrangian_mechanics