Looking through various online articles, it appears that it must be possible to use Ultegra Di2 with a single front ring, as many CX racers are using just that setup (at least at pro level). Why is this relevant? Well using a single ring, or using a manual front changer is, to a Di2 system, exactly the same thing.
I have been unable to find anything about how to do it, though, maybe dropping an email to Lennard Zinn, over at Velonews, might get an answer (from reading a few of his articles it appears he runs such a setup on [on of] his CX bike)