Hmm, I'm not sure if this is the sort of thing that should be documented with the development environment at all?
config and setting up extensions doesn't really relate to the dev environment (or in my opinion should not).
The instructions on how to install and configure WikibaseLexeme are at https://www.mediawiki.org/wiki/Extension:WikibaseLexeme

I'm OK with continuing to document here https://www.mediawiki.org/wiki/MediaWiki-Docker/Extension, we already have quite a few examples.

Hmm, Looking at https://www.mediawiki.org/wiki/MediaWiki-Docker/Extension/Wikibase for example though this is just an outdated copy of what is on the extension page at https://www.mediawiki.org/wiki/Wikibase/Installation
Infact the specific mediawiki-docker docs are currently wrong and will result in a broken install, but the extension page is up to date.

Looking at https://www.mediawiki.org/wiki/MediaWiki-Docker/Extension/WikibaseLexeme its again just a copy of the extension page and stating that Vector is needed?

I havn't clicked into the other pages but I imagine they are very much the same.
I don't see the value in this duplicated documentation and still think that the best path forward would simply be to point at the extension installation docs.

Are there any cases were fundamentally different things need to happen?

@Addshore it's not sometimes trivial to figure out how to apply extension documentation to mediawiki-docker. Take a look at my efforts for Wikibase and WikibaseLexeme. I'm pretty close for both repositories, but some Selenium tests are still failing. See T289853 and T290183.