However, when you set the "Geometry Variant" dial on the Body to 1 the geometry for each and every one of the 54 bones is picked up from the GeomSwapAlt01.obj file.

Likewise when you set the "Geometry Variant" dial on the Body to 2 the geometry for each and every one of the 54 bones is picked up from the GeomSwapAlt02.obj file.

The CR2 contains a reference to both of these files as alternate geometry for each and every bone

Each of those files contains a single object - GeomSwapAlt01.obj is the Suzanne Blender monkey head (the same as GeomSwapAlt-MONKEY.obj), and GeomSwapAlt02.obj is a very simple tuft of grass (the same as GeomSwapAlt-SIMPLEGRASS.obj).

Try overwriting the existing GeomSwapAlt01.obj file with a copy of the GeomSwapAlt-TORUS.obj file.

Try overwriting the existing GeomSwapAlt01.obj file with a copy of any OBJ file that you have lying around.

Now I'm not sure how Poser handles this internally, but I'm guessing that, when the "Geometry Variant" dial on the Body is set to 1, Poser has just a single copy of the data from the GeomSwapAlt01.obj file in memory, and has a reference to that data from each of the 54 bones.

Which is my understanding of what 'instantiation' is in 3D terms.

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The 3Dcheapskate (also available in DAZ and HiveWire3D flavours) occasionally posts sensible stuff. Usually by accident.
And it usually uses Poser 11, with units set to inches. Except when it's using Poser 6 or PP2014, or when its units are set to PNU.