force mutter to draw windows separately
Solution 1:
It looks like cssh has some options you can set for this purpose. You can add the following lines to $HOME/.clusterssh/config, which should fix the overlap:
# reserve space for the gnome-shell top bar
screen_reserve_top = <height of top bar>
# use all the space at the bottom
screen_reserve_bottom = 0
The windows likely overlap because cssh calculates the positions based on having the first row at the very top of the screen, but gnome-shell actually the first row of windows down so they don't overlap with the top bar.