That's where the Cohesion metric comes into play for OO (and maybe other programming paradigms?). Aka: is each class a single cohesive unit, or do you effectively have two (or more) classes melded together with disjoint data and methods.

Something I think is particularly interesting about this approach is that it is language agnostic. It's probably even independent of "programming". It could also be useful for general documents: if I edit wiki page A and always edit B too, should they be the same page instead?

that is partially true: single file apps will never have couplings in this manner. One extension to this project would be to find couplings between particular regions of the file and then even single file apps will start falling down. I think it is not true that if you cannot find any coupling using this tool, your software is well-designed; it would just mean this tool is not smart enough to capture those bad designs.

Couplings between different regions of the files, however, are relatively harder to find and requires some more thinking in terms of implementation.