In AtlasUtilities:CopyTexture you use the Graphics.CopyTexture method.
This method, according to the Unity documentation, is very dependent on the type of compression, and therefore a number of problems arise when repacking the skin when the atlases are compressed.
Graphics.CopyTexture can only copy memory with the same size (src=832 bytes dst=224 bytes), maybe the size (src=26 * 32 dst=7 * 8) or format (src=RGBA Compressed ETC2 UNorm dst=RGBA8 UNorm) are not compatible
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Your observations are correct, this is the reason why we document it here in the Important Note section on the spine-unity docs pages:
spine-unity Runtime Documentation: Combining Skins
http://esotericsoftware.com/spine-unity さんが書きました:2. Compression is enabled: Depending on the platform, ensure that the source texture has Texture import setting Compression set to None instead of Normal Quality.
Note that it would not be reasonable to have e.g. DXT compression enabled on the source and destination textures, since this would limit copyable regions to discrete 4x4 compression blocks.

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