Tracked down further... The bug is caused by this gnome-shell code not
running anymore:

            // This is kinda hackish - we want the primary view to
            // appear as parent of this, though in reality it
            // is added directly to Main.layoutManager.overviewGroup
            this._notifyOpacityId = newParent.connect('notify::opacity', () => {
                let opacity = this.get_parent().opacity;
                let primaryView = this._getPrimaryView();
                if (!primaryView)
                    return;
                primaryView.opacity = opacity;
                primaryView.visible = opacity != 0;
            });

because of the introduction of:

  clutter-Use-G_PARAM_EXPLICIT_NOTIFY-for-actor-and-stage-p.patch

in mutter.

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https://bugs.launchpad.net/bugs/1918874

Title:
  [regression] Application windows appear over the icon grid when Ubuntu
  Dock or Dash To Dock is loaded

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