I found that modules and themes were not detected as enabled on a D8 site.
I found why and I will provide a patch for that.
The problem is in provision/platform/drupal/packages_8.inc, _provision_system_query(),
in system_get_info() of D8, there is \Drupal::moduleHandler()->getModuleList() and it
Returns the list of currently active modules.
So firstly, the active modules are not detected because they don't have status property and secondly we do not see the uninstalled modules.