Languages defined in wmgExtraLanguageNames (InitialiseSettings.php) for Wikidata should be defined for commonswiki too, so their language support would be in sync. Languages should be working just by adding them to wmgExtraLanguageNames as other changes needed are already done for Wikidata.
Language codes to be added:
'kea' => 'Kabuverdianu', 'nod' => 'ᨣᩴᩤᨾᩮᩥᩬᨦ', 'ota' => 'لسان توركى', 'rwr' => 'मारवाड़ी', 'sje' => 'bidumsámegiella', 'smj' => 'julevsámegiella', 'srq' => 'mbia cheë',
Besides, Nyungar (nys) should be removed on Wikidata's setting as it was added to the MediaWiki core in 2018 (T182305).