All this area does is control what is displayed in the navigation (what tabs are there, what's in the sub-navigation, etc). It doesn't affect anything on the page that you're linking to. You need to implement that all separately.
Thanks @AndyB. Reading this thread was a big help. I was able to easily create a new navigation tab for our store.
The store is visible to unregistered/unconfirmed. Is there a way I can set a permission to allow unregistered/unconfirmed to see the store but not be able to buy from it, rather they would see "You must in or registered to use this section" ? In other words, they can see the store/categories/products, but can't shop unless they are registered or confirmed. I can't figure out how to do this since the store is not a XF2.0 add-on.