Usually multilingual wikis have their name as "language" on the Site Matrix

Are they intentional? Why not use mul?

No idea, but we should do it the same way for all multilingual projects.

Usually multilingual wikis have their name as "language" on the Site Matrix (like Commons, Foundation, Meta, Outreach, Species, Wikidata, Wikimania). This should be done for Wikifunctions as well.

Do you know how this is achieved? There is, of course, no documentation on https://www.mediawiki.org/wiki/Extension:SiteMatrix for how this is done.

Not sure about this. Some variables are mentioned in T329424

I would suggest use "language codes" instead of something non-language codes.

Usually multilingual wikis have their name as "language" on the Site Matrix (like Commons, Foundation, Meta, Outreach, Species, Wikidata, Wikimania).

This is exactly what breaks the sitename property in the SiteMatrix API, see T114498#9508454. (Just FYI; that issue should be resolved separately.)

SiteMatrix gets the language from the setting wgLanguageCode (link) and InitialiseSettings sets it to "en" for Wikifunctions (link).

It doesn't explicitly set it for the other wikis listed, but line 191 has 'special' => 'en', which makes it seem like wgLanguageCode is supposed to be en for those as well, but isn't, for some reason.