See for example the interwiki links on https://en.wikipedia.org/wiki/United_States and https://en.wikipedia.org/wiki/Japan, the links for mai, olo and tcy are at the bottom of the list after zh.
As far as I can tell from https://meta.wikimedia.org/wiki/Interwiki_sorting_order, it should follow the order on https://meta.wikimedia.org/wiki/MediaWiki:Interwiki_config-sorting_order-native-languagename (https://en.wikipedia.org/wiki/MediaWiki:Interwiki_config-sorting_order is set to "meta-native-languagename") but those codes are already included on that page.
Other wikis using meta-native-language as the order seem to have the same problem, e.g. https://sv.wikipedia.org/wiki/Japan, https://no.wikipedia.org/wiki/Japan (when the compact list is turned off)