Sorry for the delayed reply. If you only have 2 meshes, you don't need a PCA. For a fixed correspondence, there is exactly one deformation field, which relates the two meshes.
The PCA would in this case just have 1 component, which corresponds exactly to this deformation field.
To visualize the changes between pre and postop, I would advice you to visualize different strength of this deformation, I.e. if u is your deformation field and Gamma_R your reference,
you could plot Gamma_R + 0.5 u, Gamma_R + 1 u, Gamma_R + 2 u, etc. Extending the deformation beyond the target gives you a "caricature" of the deformation field and makes it easier to spot what is changing.