Before Symfony Flex:

• template path: /app/Resources/views/{PATH/TO/TEMPLATE.html.twig}
• override template path: app/Resources/{BUNDLE_NAME}/views/{PATH/TO/TEMPLATE.html.twig}

After Symfony Flex:

• template path: /templates/{PATH/TO/TEMPLATE.html.twig}
• override template path: /Resources/{BUNDLE_NAME}/views/{PATH/TO/TEMPLATE.html.twig}

As you can see the override template path doesn't match overall path change logic made in Symfony Flex.

Proposing to look for override templates in /templates/override/{BUNDLE_NAME}/views/{PATH/TO/TEMPLATE.html.twig}.

Right now the override folder is hardcoded in https://github.com/symfony/symfony/blob/master/src/Symfony/Bundle/TwigBundle/DependencyInjection/TwigExtension.php#L128-L130

P.S.
Might be a bug, but .../_error/404.html url is looking for override templates in /src/Resources/{BUNDLE_NAME}/views/{PATH/TO/TEMPLATE.html.twig} folder.