Drupal stores the settings a the service called settings, with class Drupal\Core\Site\Settings.
During the profile installation via drush, as the settings.php is included in a very early bootstrap stage, the settings are being initialized 2 times:
* The first time happens when the the site-install drush command runs.
* The second time is when you confirm you want to install the site (when you answer "yes" in the prompt).
Since we are running the command with drush, everything is running on the same php thread. As consequence the second time the include_once is not being executed a second time, so the settings are not being included. This can trigger undesired side-effects. For example I found the issue when trying to install a site from existing config, because the $settings['config_sync_directory'] didn't exist, but there can be many other issues.
Replace include by require
Fixed
10.0
Code
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Automatically closed - issue fixed for 2 weeks with no activity.