On my system gnome-session-properties creates a file in the directory ".config/autostart". I found out this by doing:
strace -e open,write -s 10000 gnome-session-properties 2>&1 | grep -E "open|yyyy"
And then adding a command named yyyy to the session (for testing). Looking in the console you will see where that information is written.
About .xinitrc, you can create it yourself, it doesn't have to be there.