Plone 5 Folder listing depends on types added for Search and not types added for Navigation

I upgraded from Plone 4.3.10 to 5. Then I was very pleased to use the atct_migrator to convert the basic types to Dexterity. After the conversion, I found that my Folders were listed as empty. When I navigated /folder_contents, however, the Folders and Links were there. I checked my site settings and verified that under Site Setup > Navigation > Displayed Content Types that Folders and Links were checked. They were. Then I checked Site Setup > Search > Define the types to be shown in the site and searched. The checkboxes for Link and Folder were both unchecked. After I checked them, my Standard View for my folders listed the correct content.

This is not ideal to have Folders and Links be searchable since the folders and links just provide taxonomy. I do want them to be navigable. I have many links that show up in the menu structure that point to the same target Document just from different menus. They have the same label because they point to the same Document. When the item is searched, it produces several seeming duplicates in the LiveSearch results when in fact they are distinct objects ( say three different Links to "My Topic" that point to a Document called "My Topic" ).

Is there a reason that folder navigation respects the setting for Searchable types as opposed to Navigable Types? It would seem that when navigating folders the folder listing should be based on the Navigation settings.

Has anyone else run into this? Is this just how Dexterity folders work by design, or is this a bug that I am experiencing?

Thanks to anyone who might have some advice.