While this works in an action plugin when registering the DOKUWIKI_STARTED event, the configuration manager does not reflect the changes - IMHO this is misleading. It should be possible to save the changes using config plugin's config manager classes - I'll investigate that.

$conf is global. You can change it from your plugin.

As far as I know, a plugin cannot overwrite core settings, only plugin settings. As these are core settings, those changes have to be made manually. However, even if it was possible to change the settings, I would prefer not to change settings automatically.