Your example is not a software example. But perhaps I am confused about your definition of dependency. You state it in your website and in this article as a reference in the source file. Again, by this definition, there are no transistive dependencies.
Secondly, your use of complexity science to justify your product is very suspect. Perhapas you should instead categorize this under "Systems Theory". Complexity theory is primarly focused on the simple generative rules that create these complex systems, it has little to say about the resultant complex system, it is systems theory that has been devoted to the study of the complex interconnected networks you describe.
In additon, your "case studies" and white papers make wide claims about productivity increases and the benefits of keeing dependencies low. You however make no reference to ANY justification to these claims.
interfaces are often used to break a dependency between two objects, yet one clearly exists that your product does not account for. As a quick example, classA implements B, and classC calls a method on B. Class C depends on class A behaving a certain way as prescribed by the interface, yet there is no reference in the source or class from C to A.
Perhpas your definition of dependency needs to be clarified?
I have no doubt that your tool helps in the understanding of a system. But the claim that code metrics have any bearing on code quality, maintainability, and performance is far fetched.