It appears that T11360 has added support for setting the language for individual pages. One of the suggestions (first "contact the development team" link, timestamp "06:28, 22 June 2016") was to add support for that and then make it so that Wikidata allows multiple sitelinks as long as each page's language is different.

If something similar could be done for projects (so that Incubator and the 6 affected Wikipedias can correctly mark which project a page belongs to... most wikis would just set it site-wide), perhaps Wikidata could make it possible to allow multiple sitelinks as long as the page's language and project are different. That would cover all the cases I've documented (including Incubator, Beta Wikiversity and Multilingual Wikisource) with the exception of Commons namespaces.

For example, bar:Spruch:Neil Armstrong, despite being on barwiki, would have its project set to Wikiquote, which would distinguish it from bar:Neil Armstrong. Likewise, incubator:Wp/jut/Afrika would have its language set to jut and project set to Wikipedia and that would distinguish it from incubator:Wy/cs/Afrika (which would have its language set to cs and project to Wikivoyage).

Plus, since the page would tell us which project it belongs to, we could display the pages under the correct heading on Wikidata pages and include them for the right project when generating interwiki links (e.g. q:de:Neil Armstrong should have an interwiki link to bar:Spruch:Neil Armstrong).