I think they're supposed to, to deal with pluralization, possessive, and other similar constructs. For example, if you have multiple "Foos", the "Foo" should still highlight. Or if you have something of "Foo's" or if you're "anti-Foo", it should still highlight.
After 1.0, it'll be nice to have the ability to generate links separately from the dialog text. It just causes endless problems for dialog. My idea is to have an extra field in the CS to specify a list of "follow-up topics", which when present, causes the engine to bypass the normal auto-link generation and instead you'd get something like:
"The dialog text is here. I can have anything here and it won't have links. I don't need to spell out the topics I want either, making more natural dialog.
[Follow-up: Topic1, Topic2, Topic3, ...]"
It would be different from the choice mechanism in that it wouldn't block using the topic list or Goodbye button or anything. It's just a list of topics that would naturally follow the intended conversation, but you aren't forced to use them if you want to ask about something else (the choice mechanism is still there if you want to force specific responses).