The initialiseApp method of JApplicationCms class has this command (https://github.com/joomla/joomla-cms/blob/staging/libraries/cms/application/cms.php#L630)

$this->config = JFactory::getConfig();

I think it is a mistake because it will reset all the config data which is initialized before in JApplicationWeb using $this->set method (JApplicationCms extends JApplicationWeb). For example, with the above command, the entire code in this method is useless https://github.com/joomla/joomla-cms/blob/staging/libraries/joomla/application/web.php#L1103-L1191

I tried to remove the mentioned line of code and my local site still works well. Plus, we can now accessing to configuration data intialized in JApplicationWeb with these sample code:

$app = JFactory::getApplication();

echo $app->get('execution.datetime');
echo $app->get('uri.request');
echo $app->get('uri.base.full');

Before these commands return empty.