I have found this interesting report Commercial Market Assessment for Crew and Cargo Systems Pursuant to Section 403 of the NASA Authorization Act of 2010 (P.L. 111-267), published in April 2011.
In Appendix B there is this text:
For the Falcon 9 analysis, NASA used NAFCOM to predict the development cost for the Falcon 9 launch vehicle using two methodologies:
1) Cost to develop Falcon 9 using traditional NASA approach, and
2) Cost using a more commercial development approach.
Under methodology #1, the cost model predicted that the Falcon 9 would cost \$4 billion based on a traditional approach. Under methodology #2, NAFCOM predicted \$1.7 billion when the inputs were adjusted to a more commercial development approach. Thus, the predicted the cost to develop the Falcon 9 if done by NASA would have been between \$1.7 billion and \$4.0 billion.
SpaceX has publicly indicated that the development cost for Falcon 9 launch vehicle was approximately \$300 million. Additionally, approximately \$90 million was spent developing the Falcon 1 launch vehicle which did contribute to some extent to the Falcon 9, for a total of \$390 million. NASA has verified these costs.
After this there is the key statement:
It is difficult to determine exactly why the actual cost was so dramatically lower than the NAFCOM predictions. It could be any number of factors associated with the non-traditional public-private partnership under which the Falcon 9 was developed (e.g., fewer NASA processes, reduced oversight, and less overhead), or other factors not directly tied to the development approach. NASA is continuing to refine this analysis to better understand the differences.
And to be fair, it finishes:
Regardless of the specific factors, this analysis does indicate the potential for reducing space hardware development costs, given the appropriate conditions. It is these conditions that NASA hopes to replicate, to the extent appropriate and feasible, in the development of commercial crew transportation systems.
The question: Has NASA published any reports, or updates, recently saying that they (hopefully) understand better the apparent problems of their cost models and how they have adjusted their models for the future?
To be clear, I'm not looking for SE member's opinions of why their model over-predicted the Falcon 9 development cost. Nor am I looking for any entertaining display of wit regarding well-worn NASA jibes, I can go elsewhere to find that easily. What I'm looking for is published output that says, from NASA, what they've learned.