Have you considered using IETF BCP 47 language tags instead of ISO 639-3? Every language with an ISO code also has an IETF code (usually the same, since IETF draws in ISO 639 among others). But other than ISO 639, you can do finer-grained distinctions with IETF tags. That’s why all the internet standards (such as HTTP, HTML, XML) use IETF BCP 47 instead of ISO 639. For example, Brazilian Portuguese, Sursilvan and Zürich German have IETF language tags but no ISO code. If LinguaLibre is asked to support languages without an IETF code, you can request the addition of a language tag.

For languages that have no language code yet, perhaps Lingua Libre could use “mis-x-Q12345” (where Q12345 would be the Wikidata item for the language of the pronunciation audio). That would be a syntactically valid IETF BCP 47 tag, and you wouldn’t lump unrelated languages into the same category. Once the language does get a code, some bot could change the categories of uploaded files on Wikimedia Commons. @GerardM, what do you think?

What have iso codes with Commons categorisation to do? ie a non-issue as far as I am concerned

This approach seems interesting. But if we decide to change the categorisation that way, we should start using BCP47 tags instead the ISO-639-3 language code everywhere else for consistency. As it will be a major change, I'll make a RfC on LinguaLibre, to be sure there is no opposition.