TC shouldn't have any issues with the latest version. Allthough some functions ain't working (resize shortcuts, resize web bookmarks, show or hide shortcut backgrounds) if user has CSSU installed.

Instead what makes user confused is which transitions.ini file to edit. Wiki says you should only edit one located at /usr/share/hildon-desktop, but if user has transitions.ini located at theme's folder, it's gonna take over the one mentioned before.