Actually, I think it's mentioned in the "odd note" that the Emperor was killed. I'd like to see the time set to around 8:00 the next day, though, if you take the "by other means" path. On that note, has anyone had issues with the Prison option? For some reason, it doesn't stick me in the cell like it should.
Hmm...when I played I never found the "odd note". I guess it's possible that I didn't read the ReadMe carefully enough, though...It's also possible that I'm confusing it with the alternate start that CMD made (which is no longer available on Nexus). Yes, that must be it - I first used Cliffoworm's mod for one game and then CMD's for another. In CMD's mod the emperor and his sons were still alive, but dialogue and books pertaining to their deaths had not been updated and I tried to made a patch for it, which was only partially succesful.
Come to think of it it does make things much simpler if the emperor is already killed when you start the game. Since Start Choices is supposed to have problems (the details of which nobody seems to be able to provide) with All Natural, maybe I'll go for Cliffworm's mod in my upcoming game after all...
CMD's mod also had the problem that when the first time my character got arrested in the Imperial City she ended up in the Bruma prison.