If this is still interesting for anyone (I forgot that this was still open) then the "solution" was to set the meta tag for iPhones to:
<meta name="viewport" content="width=320"/>
This ensures that the iPhone scales the content up to fit the 640 pixels (or more) the screen has, and the emojis with 16px size will now be twice as big. However, this will only scale them up to a reasonable size. It still doesn't fix it for the people wanting to control the font-size completely.