It seems that I am only provided a choice of opening windows at the left side or the center of the screen. Is there a way to force windows, or individual windows, such as the home folder to open somewhere else on the Desktop?
With MATE that's a bit more difficult. With KDE you could easily do that through the application menu.
For MATE you could use a script to start your application, then put it in place with wmctrl or xdotool. Or perhaps, if it still works on MATE, you could devilspie to (clumsily, but still) achieve something similar as with KDE to set defaults for where application windows appear.