You may check the pictures on this address: http://therion.speleo.sk/wiki/doku.php/contrib:externalviewers
In the middle of page is comparison how different viewers render PDF using closing of objects to "transparency knockout group".
Adobe Reader renders the PDF correctly, Skim renders is exactly as FoxIt - ignoring transparency knockout group.
see attached pictures
May you check it please?
In the red circled areas you may see translucing the small rocks through big blocks above.
How I may send you better and correct file? The Skim removed transparency knockout group when saved file with notes.
I cannot say anything about any of this, as the PDF is rendered by Apple's PDFKit, completely out of our control.