Language links added by Wikidata are currently stored in the parser cache and in the langlinks table in the database, which means they work the same as in-page langlinks but also that the page must be reparsed if these wikidata langlinks change. The Wikidata team has proposed to remove the necessity for the page reparse, at the cost of changing the behavior of the API with regard to langlinks.
Gerrit change 59997[1] (still in review) will make the following behavioral changes: * action=parse will return only the in-page langlinks by default. Inclusion of Wikidata langlinks may be requested using a new parameter. * list=allpages with apfilterlanglinks will only consider in-page langlinks. * list=langbacklinks will only consider in-page langlinks. * prop=langlinks will only list in-page langlinks.
Gerrit change 60034[2] (still in review) will make the following behavioral changes: * prop=langlinks will have a new parameter to request inclusion of the Wikidata langlinks in the result.
A future change, not coded yet, will allow for Wikidata to flag its langlinks in various ways. For example, it could indicate which of the other-language articles are Featured Articles.
At this time, it seems likely that the first change will make it into 1.22wmf3.[3] The timing of the second and third changes are less certain.
[1]: https://gerrit.wikimedia.org/r/#/c/59997 [2]: https://gerrit.wikimedia.org/r/#/c/60034 [3]: https://www.mediawiki.org/wiki/MediaWiki_1.22/Roadmap