Re-enabling the forward/back button causes the urlbar to coverup "more tools", burger menu, etc
The box around the urlbar is moved to cover up the "more tools" button and/or the burger menu (anything to the right of the url bar, really) if the forward/back buttons are re-enabled (anything to the left of the url bar).
However, they are also only covered up when the url bar is inactive. If it's active, they'll show.

I'm not 100% if I understood this correctly, but re-enabling the navigation buttons as well as the menu button doesn't yield any overlapping issues for me. :/
That's ... weird. I even tested this with a fresh copy of your css and only re-enabling the forward/back buttons. That being said, your screenshot does not show the "more tools" button (the chevrons). I used the burger as an example but that was kinda of hastily concluded. I did one test that I don't even remember where it also affected that. I don't use the burger menu and couldn't care less about it. Are you able to replicate this in respect to the chevron button?
Could you please check out the rework branch and let me know if this issue still persists for you? c: