If the Global Coordinate System for the two parts is different, I would just add a Coordinate System to each of the parts, so that they will be in the same place.
Reference Geometry -> Coordinate System
Pick your X,Y,Z
Repeat for the second part
Then you can change how you align the parts to the new coordinate system in the "Compare" dialog box.
(In this example, I created the two parts different, but I made the new Coordinate System from one of the parts match the Global Coordinate System of the other part.)