I hope I'm not over-thinking this, but I have a question about good answering.
The question in question is Where have the Keyboard Layout Options gone in Ubuntu 13.10?
I think the simple answer is that the settings are no longer exposed by System Settings.
One user has mentioned in a comment that
gnome-tweak-tool can handle these settings and has been encouraged to put this in an answer. I don't want to take that opportunity away from that user.
It's also possible to change these settings using
gsettings, or xkb tools.
I was about to post an answer about
dconf-editor (and how to find a list of the needed settings syntax), but then realized the OP says he knows how to do all of that and it's not what he wants.
On the other hand, some readers may not want to pull in the dependencies from the tweak tool; but may not know how to makes the changes in
dconf-editor or what the proper strings are.
I'm hesitant to submit this answer only to be told that it doesn't answer the question since the OP already knows it, but I think it's good info to get out there. So I'm asking for advice.