If a comment has
[short title](http://lo-o-ong.example.com/url) link, then
http://lo-o-ong.example.com/url is counted towards the total comment length limit.
The answer to the same issue (to ignore the link URLs) is: the current limit is enough, or to span a comment over several physical comments, or to use URL shorteners.
The current limit is especially limiting for non-English URLs. Compare the markdown for:
vs. the same article in Russian:
Shortened URLs are bad. Writers have to obfuscate their URLs. Readers don't see where they go. Links often serve as a reference to additional material so we shouldn't discourage comments that back up their statements with references.
How different is this Russian Wikipedia link from an obfuscated one?
The rendered version looks like this: ссылка. Hover over to see the decoded url:
http://ru.wikipedia.org/wiki/Вычислительная_сложность (it is clear if you know Russian — the assumption is that the links are used on Stack Overflow на русском where people do understand Russian) that it is less obfuscated than a shorten url e.g., ссылка (