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The GCP realignment process only does the image based results. The OBJ, LAS and TXT are not reprocessed.
In general you are going to get your best results by using 80% overlap (you are using much less than this) and picking 4-6 fixed points around the perimeter of the area. Then tie those points together in GIS software to compare the values. Cloud Compare is also another cool software for doing this which will let you calculate the differences between the two (or more).