Here is a follow up of the issue.
Now that the previous issue is closed, enabled modules/themes/profile are well detected on Drupal 8 site.
Now we need to detect disabled modules/themes/profiles.
I will try to provide a patch for that. It will change the _provision_system_query() in provision/platform/drupal/packages_8.inc
I found for modules and themes. I am searching for profiles how D8 detects its.