I forgot to mention that I am using no login manager, just startx from console which starts the i3 window manager via .xsession. I3 WM has very good support for various WM hints, similar bugs often mention tiling window managers, but not a specific one.
Therefore, it seems to me that it might be some setting that a login manager or DE sets and a minimal setup does not. If that is the case, it should be handled by /etx/X11/Xsession.d/ files so that every X session has it correctly enabled. This bug is very inconvenient, it makes GTK3 apps hard to use, so maybe the severity could be bumped if applicable. Kind regards, Ondřej Grover
