"People need to be able to search these without having to look inside each TOC book."
Sorry, but I'm not a huge fan or user of this "New kid on the block" Responsive layout. So it may be that I'm misunderstanding simply because I don't regularly use it. From what you are saying, it sounds to me as if you (or more accurately your users) are not able to click on the right side where it says "Getting Started" or "Email Campaign List" and see those topics open and show the content with the search terms highlighted?
As for the "bookmarks", those are normally hidden from the user and will not be searchable unless the bookmark name also appears as text inside the topic. Although, if the two are different, you could likely make it happen by adding the bookmark name as a search keyword in the Topic Properties.

At any rate, I sense that at this point I may simply be frustrating you and you may need another person to try and assist that will likely understand the issue better.
Sorry I wasn't able to help.
Cheers... Rick 