There is some benefit to using external morph data. If you have two figures (say two Sydney G2 figures) in the scene, the actual morph data will be stored only once. This saves both hard disk space and memory.
The two Sydney figures can have different morph dial settings, but the actual morph data remains the same, that is why this works.
Second, a PMD file contains the morph data in binary format, which is far more efficient than in text format. The total disk usage with PMD files is significantly less than incorporating everything in the .pz3.
Third, using PMD files to distribute morph data is one of the legally acceptable ways to do so (see the e-frontier EULA). Distributing them as .OBJ files can land you in hot water.

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