I'm using xmonad as my wm.
In some use cases, starting polybar after xmonad put polybar above windows, even with the correct configuration on both programs (without xmonad avoidStruts hook).
In xmobar, the option lowerOnStart = True is used to fix this.

Solution: Add lowerOnStart options support to polybar, which, if set true, will start polybar on the bottom of window stack.

ArchLinux
polybar 3.4.3
Features: +alsa +curl +i3 +mpd +network(libnl) +pulseaudio +xkeyboard