Tested on Fedora 19 Beta RC4, with GNOME 3.8.2.

The Region panel is capable of setting the user's input method preferences systemwide (and, indeed, does so transparently if there is only one user account, and it's an admin user). But when it does this, it removes existing XkbOptions lines.

To reproduce: install F19 Beta RC4. In anaconda's Keyboard pane, configure English (US) and French (France) (alternative) layouts, and configure a key combo to switch layouts (e.g. 'both shift keys'). After installing, go through g-i-s without touching the input source config at all, and once you reach the desktop, examine /etc/X11/xorg.conf.d/00-keyboard.conf. It will look like this:

Section "InputClass"
        Identifier "system-keyboard"
        MatchIsKeyboard "on"
        Option "XkbLayout" "us,fr"
        Option "XkbVariant ",oss"
        Option "XkbOptions" "grp:shifts_toggle"
EndSection

Now go into control-center's Region panel and add another keyboard layout (I used German). As we have a single admin user, there's no 'Login Screen' panel, this change gets applied systemwide via localed transparently. So examine /etc/X11/xorg.conf.d/00-keyboard.conf again, and it looks like this:

Section "InputClass"
        Identifier "system-keyboard"
        MatchIsKeyboard "on"
        Option "XkbLayout" "us,fr,de"
        Option "XkbVariant ",oss,"
EndSection

Note the XkbOptions line has gone. I think this may _possibly_ be fixed by https://git.gnome.org/browse/gnome-settings-daemon/commit/?h=gnome-3-8&id=cf544fcd647a9e2efe86fe58f11d8f57d908f202  but I'm not entirely sure, so I figured I'd report it to make sure it's not lost.

Destroying an element of the user's systemwide configuration entirely without notice seems kinda rude, so setting 'major'.