That's a good observation. Since making this post I bought the Royal Court DLC that lets you hybridize cultures, and I found that "Naming practices" are part of the aesthetic options for cultures.
I have the same primary titles on my current run as I did on my previous run, but this time I have a Russian-Finnish hybrid culture instead of straight Finnish; and my titles are Tsardoms and Grand Principalities instead of Empires and Duchies.
EDIT: After playing around with it some more, I'm pretty sure it's the Heritage that determines the name of titles, regardless of Naming Practices. On my new run I have an Afghan/Rajasthani hybrid culture. Upon adopting the Iranian Heritage from the Afghan culture, my title switched to Shah, despite retaining Rajasthani Naming Practices and the Gurjar language.
I guess I could try to imprison her, save-scum to make sure she refuses, win the war against my tyranny, and then revoke her title as valid punishment for revolting against me. But that would be wildly out-of-character and senselessly destructive. I really hope there's another way I'm not seeing.