actually nothing about it is hardcoded in the themes. as usually. there's one AFAIK ('Green Marine') that has its own one.
as I already wrote in http://en.forums.wordpress.com/topic.php?id=1815&replies=19#post-10083 about 9 months ago, it's just a matter of adding another dozen lines of spaghetty code to the big ball of mud. all it needs an uploaded image, pretty much the same as avatars handled.
nice try is to send in Feedbacks with requests of 'Custom FavIcon/FeedIcon'.
btw, current default WP.com Favicon (and hence all wp.com feeds FeedIcons) is just terribly ugly (striken) visually challenged: that somber black logo may well suit for some heavy-metal fan's t-shirt, but it makes me really down, especially when I can see several of such in a row in the feed-reader.
not speaking it uses a non-transparent (white) background around its black circle which makes it even more miserable.
may be we could have some contest for the new in something more cheerful colours one?