The fact that Apple decided to tackle this on iOS, an OS used on handheld devices which are typically viewed at closer distances, tells me that it’s something they feel is worth doing when you have the display resolution to do it right.
SmartUnderline makes a similar assumption, not applying itself to links with a small-enough font-size computed style.
With respect to your [edit] block:
> Obviously, it's a lot easier to fix this issue with a single font, as Apple has done in Messages.
Apple has implemented this throughout iOS 8, not just in Messages. Here’s a screenshot of Safari [1].
> I'd rather not have to worry about the background, font and select background colors for every link.
That’s actually the beauty of SmartUnderline. It figures all of these things out for you, automatically [2]. Please let us know if you run into any trouble though. :)
[1]: http://postimg.org/image/4ncgrezxr/
[2]: http://git.io/9YNfgg