The only thing that really bothers me personally about shorteners is not knowing where I'm going to end up, and not being able to identify articles I've read before. A shortener with a dedicated domain and user-chosen ids should cover that just fine. The only outstanding issue in the article is a single extra DNS lookup, which is pretty minor compared to the massive chains which were causing the problem.
There's an additional security issue when a URL shortener is abandoned and malware groups pick up the domain.
If the shortener is tied to a site than why is that risk any greater than the risk of the site itself being abandoned?
Using it yourself isn't the same as instructing other people how to do it.
Using it for a personal domain is likely going to hurt your SEO. You can track behavior on the server side without JS just as easily without short URLs.
However, this is a personal domain for my use only. And I don't think you can simply dismiss the usefulness of being able to track link usage and referrers without using nasty client-side JS stuff.
I'm also using "shortcodes" rather than random IDs for most stuff so the intent isn't lost.