I questioned Coding Clinics directly regarding clarification on this issue, and just received their response:
"ICD-10 CM presumes a casual relationship between two conditions when they are linked by the term "with" . The word "with" should be interpreted to mean "associated with" or "due to" when it appears in a code title, the alphabetic index, or an instructional note in tabular list."
The example they give then is:
Diabetes, diabetic (mellitus) (sugar) E11.9h
with
amyotrophy E11.44
arthropathy NEC E11.618
autonomic (poly) E11.43
cataract E11.36
Charcot's joints E11.610
chronic kidney disease E11.22
circulatory complication NEC E11.59
complication E11.8
specified NEC E11.69
dermatitis E11.620
foot ulcer E11.621
gangrene E11.52
gastroparesis E11.43
And so on
"The sub term "with" in the index should be interpreted as a link between diabetes and any of these conditions indented under the word "with". The physician documentation does not need to provide a link between (for example) the diagnoses of diabetes and chronic kidney disease. This link can be assumed since the chronic kidney disease is listed under the sub term "with".
These conditions should be coded as related even in the absence of provider documentation explicitly linking them, unless the documentation clearly states the conditions are unrelated and due to some other underlying [cause].
So I guess that settles it then? I goes against everything I was taught but there it is. When I read the instruction regarding the word "with" I still assumed this meant in the documentation, but apparently it was a misinterpretation based on years of training regarding the documentation must link the conditions.