How to Set a Central Point of Interest in ContextCapture for the comparison of two different 3D meshes of the same object

I'm trying to compare the difference between two different 3D meshes of the same object.

For instance, let's say the object is a bookshelf. In the first 3D mesh generated by ContextCapture, the bookshelf will be completely full of books. In the second 3D mesh, the bookshelf will have some books removed, and perhaps a hat or some other random item will be placed in some of the empty space.

So far, I have used a camera, dolly, and tripod to ensure that my photo datasets for each reconstruction are very similar. But upon generating the 3D meshes, even after using tie points, scale constraints, and adjusting the boundary, the 3D models do not align themselves. Is there a way to define a central point of interest on the model, so that when I import it into a mesh/point cloud comparison software, the models will overlap (be superimposed on top of each other? 

As an aside, if anyone is aware of the best way to compare 3D meshes, please let me know. As of right now, my best solution has been to generate point clouds using the data set, and then use the point cloud differencing tool provided by Pointools.

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