I agree with you entirely- I think the 'case study' presented is an example of the interference effect based on the slow progression. My own background and training means I lack perspective for multi-modal athletes (OCR, military, MMA, CF, etc.: would sequential or concurrent training be best for them?
Sorry for making assumptions (and this addresses Brodie's question): the N=1 was a CrossFitter- his training, according to the author, was concurrent (CF). He was 160# with a 6:57 mile run and a 135# snatch starting off. The snatch PR and run were taken close to each other.
Again (because I realize I wasn't clear enough earlier), the interference effect seems well established- this case study is not even worth holding up to challenge it. I bring it up as a point of discussion: how do we get around it? If you were training a CF'er or someone who, eventually, has to dip into the aerobic spectrum for their sport, how would you do it?