Thread position is calculated even without the PID.

In Drupal 8 beside the PID there is a thread column in the comment fields table, Drupal uses this column to render the comments so even that this module removes the Parent ID as expected the comments still save a reference of the thread and therefore the comments are not completely flattened (the module can be uninstalled or have the Threading option selected and the comments will be displayed as a thread).

So, it is necessary to recalculate the thread before to save the comment to guarantee that even removing the module or restoring the "threading" option the comments created without threading are still flat.