Should drush configuration export automatically update core.extension.yml?
I think that the problem comes from where you have the config files, to be sure that they are really in the config/sync folder go to check if you have this following line in the settings.php file:

$config_directories = array(CONFIG_SYNC_DIRECTORY =&gt; 'config/sync');


Keep in mind that this line will have the location of the site configuration files.

Each time you use the drush cex or drush cex sync command the core.extension.yml file will be updated (if needed) with the actual modules (and others) configuration.