Webform entity select submission displaying different result than element
I was able to get the desired result for the book title by using twig and string manipulation. 

I noticed {{ item.label }} returns MyBookFieldCollection 0 of Dune. MyBookFieldCollection is the name of the field collection and 0 represents the selected item. There will not be more than five items in a given collection. I can remove the start of the string using {{ item.label[27:] }} and this returns a value of Dune.

Here is the modified element source:

book_title:
  '#type': entity_select
  '#title': 'Book Title'
  '#select2': true
  '#format': custom
  '#format_html': '{{ item.label[27:] }} - [webform_submission:values:book_title:entity:field_isbn_13] - [webform_submission:values:book_title:entity:field_format]'
  '#format_text': '{{ item.label[27:] }} - [webform_submission:values:book_title:entity:field_isbn_13] - [webform_submission:values:book_title:entity:field_format]'
  '#target_type': field_collection_item
  '#selection_handler': views
  '#selection_settings':
    view:
      view_name: entity_reference_for_form
      display_name: entity_reference_1
      arguments: {  }


This outputs Dune - 9780441013593 - Paperback in the form submission.