But they are presenting the methodology they claim went into the code and allowing you to agree or disagree with the methodology. If you agree, you take their answer, if you disagree, you implement a different methodology, which necessitates new code anyways, and publish your contra-finding.
We usually converge on answers over years of varying different methods and attempts. No one in their right mind reads a paper and says "well, they found out the sun is actually in M31, I believe that now" They look at the culmination of the literature (fun fact, we still aren't positive exactly where the sun is, or how fast it's moving) and I suppose that is the black box.
What I was really referring to though was students who walk up to me and say they gaussian smoothed a sample, and have no idea what I mean when I ask if 3 sigma outliers were used in the fit or trashed. They just used some gaussSmooth algorithm and may or may not know what a gaussian even is.