Roll on to January this year and my pre-ordered XTR rear derailleur finally arrived. Yay!
I got some answers from Shimano about this, and I now know that you cannot mix any road FD (front derailleur) with an XTR Di2 (11-speed) rear derailleur (RD-M9050); it won’t work with any Di2 shifter, road or MTB.
I just had chance to experiment and this does indeed seem to be the case. Plug in the XTR rear derailleur on its own with the Dura-ace levers and it works a charm. But plug in the road front derailleur and the entire system seizes to a halt. No shifting on either end, no battery indicator, nothing. So as Leonard says the options are to convert the drive-train fully to XTR (both the RD and FD) or run it 1x11 speed without a FD. Neither of those options are good for us, as we want the much wider range you only get with the road FD (strange but true: the road double FD has a wider range than the MTB triple). Or else I guess, we could buy a second battery and run the front and rear derailleurs as completely independent systems. Yuck!
OR of course, plead with Shimano to issue a firmware update to allow this configuration! There's no electronic reason for the incompatibility, merely a policy decision of them wanting to enforce that the entire the drive train (derailleurs chains and cogs) are all from the same family. Unfortunately, electronic shifting and complex firmware configurations has increased the means through which they can enforce what are basically business decisions.
In the meantime, if you're in the market for a never used XTR rear derailleur let me know...