I'd call this a bug. At the moment index.template.php, for both 1.0 and 1.1 beta, has this code up in head.
<link rel="shortcut icon" sizes="196x196" href="' . $settings['images_url'] . '/mobile.png" />
Problem: that is theme-dependent. If someone has a bunch of themes installed, they need to put a custom favicon in every theme's images folder. This is a PITA. Why not code it like this instead?
<link rel="shortcut icon" sizes="196x196" href="', $scripturl, '/mobile.png" />
That way, one image in the forum root folder does all themes. Easy. This is also the behaviour people will expect anyway, since it's the way favicons have been done for years.
The other point, which I personally haven't tested so can't confirm yet, is that according to some sources just using one link rel won't cover all operating systems and browsers. See: http://stackoverflow.com/questions/30824294/mobile-favicons#30839701
This would imply that to cover just desktop and Android/iShiz (and who cares about IE) you would need two link rel's.
<link rel="apple-touch-icon" sizes="32x32" href="' , $scripturl, '/apple-touch-icon.png"/>
<link rel="shortcut icon" sizes="32x32" href="' , $scripturl, '/apple-touch-icon.png" />
AFAICT that should work, since desktop browsers don't care what the image is called, as long as it's a png and is named in the link rel.
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