Right, "protocol" in that sentence meant "Wayland protocol". I'd forgotten about AT-SPI, and it's true that it solves that problem, though it seems that it also includes API for synthesizing input which would require the compositor to implement something.

>I'm wondering if there is a way to somehow get active window position, move windows around etc. using root privileges

Root doesn't matter, because the compositor isn't running as root either. ie being root won't give you any more privileges over it that just being the same user doesn't.

Things like "active window position", "move windows around", and even the entire concept of "windows" are internal to the compositor. Wayland only talks about surfaces; what the compositor does with those surfaces is up to the compositor. It might display them as windows, or as sides of a 3-D rotating cube, or print them through a printer. So you're not going to get that information from anywhere other than the compositor.