Which is a shame, I do dearly like xdotool etc. There should be a way to satisfy both security and function, a way to whitelist or permit special apps.
Nice choice of words here. The whole reason why it isn't supported is to prevent being hacked in the first place. X11 has no security whatsoever. Every window can read/spy/mess with any other.
I guess only window managers / compositors will have enough permission to do this level of automation.
Typically a root windows is the same as a screen, but i don't think there is anything that claim this to be a set in stone rule.
But as is typical of Linux GUI devs, they much rather hack on the new shiny than try to maintain the existing stuff. And the new shiny these days is to put everything on the GPU.