I don't know what happened but it's not working.
We rewrite /favicon.ico to /w/favicon.php. Which is a custom MediaWiki entry point that initialises MediaWiki WebStart and streams content from the url configured in $wgFavicon.
This is a public endpoint used browsers (when there is no <link> tag), but also my various of our own websites – inside a <link> tag in fact. E.g. <link rel="shortcut icon" href="//wikimediafoundation.org/favicon.ico">.
I've tried executing the main steps from the script manually from mwscript eval.php --wiki enwiki on tin, but it works fine there.
https://github.com/wikimedia/operations-mediawiki-config/blob/master/w/favicon.php