The addon already works for traditionally modeled objects that are later deformed or animated with Geometry Nodes modifier.
But if you want to use it on an object completely created inside a GN setup you can use this method.

How to use SPM with objects created entirely inside a GN node group

You will have to manually overwrite the rest_position attribute in your GN setup in order to let the addon know what the objects rest position should be.

1. Identify the part of your setup where the object is on it’s rest position (geometry is finished but still not animated or transformed).
2. Replace the rest_position attribute as shown in the example.
3. You can make any animation or deformation after the attribute replacement.
4. Assign the material using SPM node using a Set Material node.

Example of a simple object created by a boolean mesh between a UV Sphere and a cube

A- We identify the finished object without any transformation (object in rest position).
B- We replace the “rest_position” using a position node and a store named attribute node.
C- This is a simple animation test created AFTER the rest position was replaced
D- We assign the material that will be using SPM node.

The material used in the example

Final result

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