The only other thing I can think of is that all of Cass's greetings are followed by specific selection of topic choices, rather than a topic list to which the sandbox topic has been added.
Damn, I just checked and this is exactly the problem. Pretty stupid, as it'll make things very difficult for any mods adding dialogue to Cass. If just one does it by adding a new choice it's fine, but it probably would cause conflicts if multiple mods would do it that way.
Unless everyone would stick to normal topics, and one mod would remove remove all the topic choices and let it add the vanilla topics to the normal list instead, but I'd have to be careful not to break anything.
They didn't pull off this seemingly pointless crap for the other companions. Thanks Obsidian!
It's especially annoying since I'm considering a different dialogue based mod for companions, so if I take the lazy route now and just add a topic to the choice list it's going to conflict with that mod.