To address your concerns about exporting PNGs from Spine and managing their size in Unity, here are some steps and tips:

1. Exporting Based on Folders:

   • You can control which images are grouped together on the same atlas page by organizing your images into subfolders. When exporting, Spine will create separate atlas pages for each subfolder. This should help in creating two PNGs based on your two main folders.
   • Refer to the Texture Packing - Spine User Guide: Folder structure for more details.

2. Reducing PNG Size:

   • Use PNG Optimization Tools: Tools like pngout or pngcrush can help further compress your PNG files. Ensure that your game toolkit can still open the resulting PNG files after compression.
   • Reduce Bit Depth: You can reduce the bit depth from 24 bits to 8 bits, but this will limit the colors to 256. This can be done using tools like Photoshop or opt-png in littleutils.
   • Scale Down Textures: You can scale down the texture atlas during export. This will reduce the size but may affect the quality. You can do this by adjusting the scale settings in Spine.
   • Use Binary Export: Export your data in binary format and compress it using algorithms like deflate, lzma, or lzo. This can significantly reduce the file size.
   • Premultiply Alpha: Ensure that your PNG files are exported with premultiplied alpha if your compression tool respects PMA. This can help in maintaining the quality of transparent areas.
   • Adjust Texture Import Settings in Unity: Ensure that the texture import settings in Unity are optimized. Disable compression if it causes issues and ensure that the textures are set to full resolution.

3. Runtime Repacking:

   • If you are using multiple pages, you can repack the textures at runtime. This is useful when you have many costume differences and need to change them dynamically. Refer to the spine-unity Runtime Documentation: Combining Skins for more information.

4. Example Scene:

   • You can see a demonstration of skin combination and texture repacking in the example scene Spine Examples/Other Examples/Mix and Match Skins.

By following these steps, you should be able to manage the size of your exported PNGs more effectively while maintaining the quality of your 2D textures in Unity.

novus As Spinebot answered, it's a good idea to use runtime repacking. In other words, when you export from Spine, don't pack all images into one image, but export them as multi-page images. Then combine used texture regions of a collected skin into a single texture at runtime using the Skin.GetRepackedSkin() method.

Also, check out "Spine Addressables Extensions", which provides integration of Addressables on-demand texture loading. This is useful for speeding up the loading of Spine skeletons that refer to a large number of Atlas texture pages:
EsotericSoftware/spine-runtimestree/4.2/spine-unity/Modules/com.esotericsoftware.spine.addressables/Documentation

@novus I'm not sure I understand what your current setup looks like. In the top posting you've mentioned having a single very large atlas page texture, but in the above posting you mention having multiple materials. Could you describe what materials you currently have, what textures are assigned at each material? Do you have one large atlas page texture and use multiple materials with the same atlas texture? If so, what is each material used for?

Will this get affected by multi-paged export and runtime repacking?

Exporting as multiple atlas pages instead of a single atlas page multiplies the number of materials, yes.
Runtime repacking reduces multiple atlas page textures to a single texture (unless you repack multiple skins separately or multiple lists of attachments separately, each to a single texture). I'm not sure what your materials are used for, so I can't describe the effect it has on your project.

novus Currently our Spine image folder has two main folders full heads and avatar.

How can I export properly two have two png atlases one for each folder and ofcourse with the correct binary configs export.

If you have your attachment images already sorted by folder for the desired output atlas, it sounds as if your would best export based on folder structure as Spinebot mentioned above.

novus It would be better not to use the Combine subdirectories checkbox in the texture packer settings and use pack.json to ensure that only certain subfolders are combined. If you want to configure pack settings to affect only specific subfolders, you can place a pack.json describing the pack settings. For example, you can combine the subfolders under the "MainAvatar" folder by placing a pack.json in the "MainAvatar" folder with the following json:

{
    combineSubdirectories: true
}

For more information on pack.json, see the user guide: https://esotericsoftware.com/spine-texture-packer#JSON-Configuration