Question 1: I've remapped the shortcut for the "home" entry to Super+F, then I did the same to Super+E to "emacs -gui", but when I use Super+E it starts up Caja instead of Emacs. why?
Because the used windowmanager "marco" also has shortcuts defined, but these do not show up in mate-configuration-center -> keyboard-shortcuts
Here is a howto to change the keyboard shortcuts of "marco":