The request may be helpful for mostly cross sectional view to figure the whiskers (lines) between reference data set and the compared points (term from Geomagic Software). Or it's been called as vector field.
The idea, if possible to define point indices which point compared each other from reference to test data, then draw whiskers from reference point cloud to direction of second test data. And optionally the lines can be colourised by magnitude of difference.
Is it possible?