Two early thoughts as I am reading:
1. I agree with the description of empirical work as a "craft". When I teach, I always tell students that econometrics (in practice) is as much "art as it is science". And, I try to point and what points in an analysis we have left the science realm and have entered the art realm.
2. The "system" pillar and "vernacular knowledge" seem incontrovertible to me, but the "scale" part is less clear. Yes, we don't want to "sweat the small stuff". But, this requires knowledge that the "stuff" is "small". Too often researchers appeal to the "smallness" of a problem as a justification for ignoring it, but in fact have no idea if the problem is small or not. Thus, ignoring "small" stuff runs the very risk of inducing a lack of credibility. Two common examples of this are issues of measurement error and the choice between LPM/probit/other binary choice models.