Rewriting an old extension to use extension.json, I have found out that a maintenance script provided by the extension has no access in ...::finalSetup() to the extensions settings as defined in extension.json. However, the settings from LocalSettings.php are available.
It does not matter whether I try to access setting via global variables or $this->getConfig().
There is $this->requireExtension( 'my extension' ); call in the maintenance class constructor.
When MediaWiki is invoked by the web server, all the settings are available, and extension.json and LocalSettings.php are merged correctly.
Is there anything more to do?