I'm running Wayfire 0.9.0 under Artix Linux.
I've tried setting the padding, border, margin and min-height to 0px in wf-panel .window-button, wf-panel .window-button.flat and wf-panel .window-list, but still every time I open a window and the window-list appears, the panel gets taller. Window-list is the only thing that seems to do this.