I've looked at deffnetizer and ficsavers.com a bit. Neither outputs epub directly, so apparently you've already converted from html to epub.
The deffnetizer epub you posted does contain a proper story URL, but that depends on the output template used. The first two templates I tried, "Default Template" and "Minimal" do
not include the story URL anywhere.
The ficsaver.com epub you posted, as you say, contains a broken version of the story URL. Although it looks like that may only be a problem with ffnet stories.
All told:
- The user would have to have converted the story to epub;
- Then the plugin would have to scan at least the first three html files (cover page, ToC/splash page and first real page) for URLs, while;
- Checking for both valid story URLs and at least one form of broken URL;
- And even then, it wouldn't work for half of the included deffnetizer output templates.
So, while possible, it would be a bit of a pain and not work all the time anyway. At this point, I'll add it to the 'wishlist' of features I might add some day, but it's not going to be a priority.