I've been having this problem recently as well. The only way I could get it to respect the theme was to enable the Title Bar option in the Customize Toolbar settings. It's not my favorite look, but it at least matches everything else.

An easy fix would be to display the menu-bar in Firefox/Librewolf (Press Alt to display menu-bar, then enable the menu-bar under the View menu); this forces Firefox to display a “traditional” window-bar that XFWM can hijack and theme.