3D Compare is a great tool to get a simple visualization of the deviations between the reference and measured data.  If desired, it can be contained to specific reference faces.  2D Compare works in a similar way, but is constrained to a 2D section. This section can be customized to zigzag through multiple cutting planes.

The 3D/2D Compare tools have the ability to create tags.  This is useful for calling out max/min deviations. For any other method of tagging, it is better to create them with the Comparison Point tool as explained in this article.
Note: The compare results will not be affected by changes in the Pairing Manager.