Drupal installed as composer package, Custom themes/modules folder
Drupals extensions discovery looks only in some specific folders (see http://cgit.drupalcode.org/drupal/tree/modules/README.txt for more information).

But, you don't have to put your own modules inside of the core folder. You should use /modules instead.

The Drupals default directory is not ideal for a development workflow with composer in mind. Take a look at https://github.com/drupal-composer/drupal-project if you have not already.