which I'm not doing, I'm scaling the parent scene containing the mesh and collision shape.
scale is one of the properties that are automatically inherited by child nodes. You can attach a script to the collision shape and in
set_as_toplevel(true) to prevent it from inheriting the parent's scale but that is NOT something I advise doing with a collision shape since your collisions could potentially be skewed from what they appear to be. Doing so will also make you work in "transformed coordinates" relative to the parent node so it should just be a headache all around.