Where are config dependencies stored?
The error you see is output from ConfigImportSubscriber::validateDependencies(), which uses the following code.

  // Validate the dependencies of all the configuration. We have to validate
  // the entire tree because existing configuration might depend on
  // configuration that is being deleted.
  foreach ($config_importer
    -&gt;getStorageComparer()
    -&gt;getSourceStorage()
    -&gt;listAll() as $name) {

    // Ensure that the config owner is installed. This checks all
    // configuration including configuration entities.
    list($owner, ) = explode('.', $name, 2);
    if ($owner !== 'core') {
      $message = FALSE;
      if (!isset($core_extension['module'][$owner]) &amp;&amp; isset($module_data[$owner])) {
        $message = $this
          -&gt;t('Configuration %name depends on the %owner module that will not be installed after import.', [
          '%name' =&gt; $name,
          '%owner' =&gt; $module_data[$owner]-&gt;info['name'],
        ]);
      }


The code assumes that for a name like node.type.article the owner is the Node module. If the owner is not one of the installed modules, Drupal gives the error you see.

To answer your question, the module name is assumed to be stored in the configuration filename.