If I understood correctly what you're doing is:
- you didn't scale the original .png image outside of Spine
- you scaled the mesh that uses the .png image down instead
- you expect the .png to be scaled down on export
As you can read in the Spine user guide at the Freeze paragraph Meshes - Spine User Guide: Freeze
The Freeze button can be used to set the rotation and scale values to 0 and 1 respectively for the current vertex positions.
Which means that inside Spine, that will be the new normal, basic state. This was thought to help you in case you had to make adjustments to a Mesh. A mesh though, follows a path to link to a certain image, but it is not the image itself.
If you want to scale down all of your images you can export them specifying a size in the atlas settings such as 0.5 to have it half the size:
You can find out more about the export settings here: Texture Packing - Spine User Guide Export - Spine User Guide
If you just want to have the image in the mesh scaled down as long as you don't change the proportions of the image you can simply scale it down in your image editing program of choice, and Spine will automatically adapt the mesh to the new size, so that it will look as if nothign changed, as explained here: Meshes - Spine User Guide: Image resize (the same can't be said of attachments, they will look very funny if you scale them up/down)
I think what you'd want to do then is:
- scale down the specific .png that is used by the mesh you wish to see smaller in Gimp/Photoshop/Krita/...
- check that it looks how you want in Spine (better turn on Spine after you've scaled it down)
- export at the desired size
