One constant criticism of the automatic method is the inability to duplicate resulting response determined by the EQ tool via independent measurements, e.g., using REW. That is, however, an issue resulting from things like the inability to duplicate mike placements exactly in calibration vs. subsequent measurement. Also, many aspects of the algorithms used by the tool may be proprietary or unknown, such as multipoint averaging, time windowing, 1/x frequency smoothing, etc. So, independent followup measurement gets trickier with automated tools, unlike the more open and more deliberate completely manual calibration idea.
This criticism is certainly not true. I've done it many times with Dirac Live, Audiolense and Acourate. All three match up with predicted response in frequency and time domains. In the case of the Dirac Live, I even made the measurements from the exact same mic positions and averaged all of them together. I did a thread here on this and displayed the result. At that time, I used Fuzzmeasure instead of REW. For some reason the Dirac DAP messes with the sync in REW on windows and I couldn't get clean measurements through the DAP filter. It was nice and easy on a mac using Fuzzmeasure. The measurements I've done for Audiolense and Acourate were done with REW and they matched up very nicely also. DSP works well when done right.