'faviocns' are stored in ones' '~/Library/Safari/Icons/' folder and in RAM; not in any cache files.
However, I do not have a 'Mac Pro' available, and thus cannot attempt a similar scenario as freaky.
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With 'Safari' quitted, lock the 'Icons' folder (and optionally, lock - the 'Caches' 'Safari' folder), and then re-launched (open, run) - favicons will be displayed when dragged to any 'Bookmarks Bar' folders or added to the 'Bookmarks Menu'. Clearing the 'Cache' will not affect the related favicons.
Quitting and then re-launching 'Safari' will result in generic favicons displayed for the above mentioned added 'Bookmarks Bar' and 'Bookmarks Menu' related links.