On a page like https://www.wikidata.org/wiki/Q190434 (with JavaScript enabled) I see

<a rel="nofollow" class="external free" href="http://moodle.org">http://moodle.org</a>

but also:

<a class="wb-external-id" href="https://www.quora.com/topic/Moodle">Moodle</a>

The identifier link with URL formatting is treated like an internal link, which is clearly wrong. The wb-external-id class should style the link as an external link.

Additionally, when $wgNoFollowLinks = true, one would expect all such external links to be nofollow'ed unless whitelisted (e.g. by means of $wgNoFollowDomainExceptions).

If there is a desire to have an on-wiki per-domain whitelisting, similar to the interwiki map, this should be controllable together with the URL formatting (P1630). I'm not sure where the URL-generation code resides though; I think it used to be a gadget.