It is a skin so those are not eye holes. I remember this being asked in the past and the skin does not work that way.
Sorry
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The entire thing is a skin and is not made to have any transparent spots because the base would show through anyway. Those are just white holes. Sorry my mind automatically thought of eyes because that is what most people ask about on the skins.
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As far as I know the base is still there but I am not sure. I put on a skin to see if a separate layer would show so I could move both skin and base but I can't tell...it doesn't seem to replace the base. But yes Bean explained it better...the skin wasn't drawn to be layerable so it would have to be redrawn to even work. It isn't necessarily a bug that the holes are filled in, it is just how they worked when they were released.
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