How do I enable Clean urls within a migrated site?
Did you read this:

  # Modify the RewriteBase if you are using Drupal in a subdirectory or in a
  # VirtualDocumentRoot and the rewrite rules are not working properly.
  # For example if your site is at http://example.com/drupal uncomment and
  # modify the following line:
  # RewriteBase /drupal
  #
  # If your site is running in a VirtualDocumentRoot at http://example.com/,
  # uncomment the following line:
  # RewriteBase /


Actually, you should use the original D8 .htaccess cause there are some special rewrites for core and autoloader (and more).