My understanding is that "window managing" tools like this are not possible due to how wayland handles information. Pro: More secure than x11, Con: I can't use wayland. Aside from investing a lot of time learning how to use a tiling wm I dont see how I'm going to get over my addiction to minimizing only the active window. ( xdotool windowminimize $(xdotool getactivewindow) )
For improved security with X11, try firejail+Xpra, or Qubes OS. They will not just help in the graphical front, but also others like processes and storage isolation.
Besides the limitations others have mentioned users should be aware that since ydotool works by writing events directly into /dev/uinput the input will go to whatever happens to be focused at the moment. It will happily type your secrets into a chat window if you move the mouse at the wrong time.
There is no way to do the equivalent of xdotool type --window 0x600005 "my important input"
It's not like xdotool is so secure in the first place. X11 is one huge hole from that perspective. Anything can read anything and all your important input can be read by some other window anyway.
