Hallo and welcome to Sabayon, Memory.
It seems your questions 1,2,4 are rather answered. Good.
To number 3 with 2 screens, the thing is, that xorg.conf is a xdm or graphic environment describing file in which is kept your configuration, as there are your displays, mouse, keyboard and graphics device (nvidia, amd, intel..).
This /etc/X11/xorg.conf is used by your GE (here Gnome) and here you configurated to use a second display.
Before login, it is (I assume) hardware config of your computer, how to deal with a second screen.
So, I fear, there's no choice for you to use 2 screens off being logged in.
But to get 2 screen config every time you log in, you should write this config, you finished, 'as standard'.
At least in KDE 'Display Settings' (I assume similar for Gnome) there is a button you can click and save your config into:
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If you don't save, xorg.conf is generated each time, when you boot, but without second screen!
This is my experience, I used 2 screens long time though with KDE (4.9.5).
Anyway, hope to help you.
-Linuxfluesterer (I love KDE ...)
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