It tries to update (if exists) both the transitions.ini in the themes folder, and the one in /usr/share/hildon-desktop. I did not alter any of that code. The update of /usr/share/hildon-desktop/transitions.ini works fine on my device. Both in case /usr/share/hildon-desktop/transitions.ini was altered manually (theme customizer picks up that new value, only from /usr/share/hildon-desktop) and when theme customizer writes it's updates. I have tested this multiple times.