So, as I was suspecting at the beginning this would have been fixed by
latest upstream changes on the dock and so it's now fixed by
https://launchpad.net/ubuntu/+source/gnome-shell-extension-ubuntu-
dock/69ubuntu1

However, sadly, it's too late for the the input thread patches as we've
reverted them now:
https://launchpad.net/ubuntu/+source/mutter/3.38.4-1ubuntu1

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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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