Issues with address / search box and header

[jasonmarkperez]

I feel like I've been really struggling to keep my address / search bar and bookmarks toolbar in the header working consistently over updates. I had the address bar in the top bar along with plugins, and a bookmarks toolbar, and they were all shown on hover.
But, after the latest update, the address bar is shifted back to the sidebar, and I don't seem to be able to customize it back.
Honestly, I get a little overwhelmed by the various ways and places Zen has to be modified, so tried to reset everything back to a default state and removed all mods to make sure nothing was interfering.

This is what I have my customized setup:

But, this is how it looks, even after restarts, nothing happens on hover:

Am I missing something, or is this part of Zen just really buggy?