Does hildon-desktop look at /etc/hildon/theme/transitions.ini in preference to /usr/share/hildon-desktop/transitions.ini? I didn't think it did (haven't checked). Does Theme Customiser put a symlink in its place to the one inside the theme? If so, the real solution is to follow any symlinks in place on /usr/share/hildon-desktop/transitions.ini, rather than looking in different locations.