I can't find the link now, but there are two ways (I know of) for getting the xdotool way to work. One way is the Durden 'control' socket and a standalone tool 'arcan-cfgfs /path/to/.arcan/appl-out/durden/control /my/mountpoint' that is a FUSE driver. You can mount the desktop as a file system and automate everything like that: echo "typethis" > /my/mountpoint/windows/all/text/input".
Another is to expose that more generally with hookscripts (force-injected Lua scripts that override or add features to the WM you use, arcan -Hhooks/something.lua).