Funny you ask. I've had a hell of a time these past few days dealing with two bricked Di2 bikes. The official answer is that you shouldn't have any issues running that combination as long as all firmware is updated. There's a compatibility chart somewhere but basically the only thing I've ever wanted to do that I couldn't do was use a road FD with a clutch MTB RD.

I'm running the old Shimano hydro brifters with the new battery, new bar end junction, new d-fly, and the legacy XT Di2 rear derailleur. The problem came when I tried to update the firmware via bluetooth, which I had to do because when I plugged into e-tube project the software told me I could only update the d-fly firmware via bluetooth, which I guess makes sense until the bluetooth update fails, the whole system shuts down, and you can't remove the d-fly because it's in the damn down tube. I digress, but I ultimately got it all figured out by mixing and matching parts from different bikes.

If you can get the firmware updated, it should work, and if it doesn't there is probably something wrong with your parts or cables. I couldn't get my MTB working either and could not figure out why until today when I received the SM-PCE1 PC Linkage device which basically allows me to diagnose every part. This is sort of an absurd thing for an individual to have but it's not completely crazy when you do this kind of nonsense with bikes regularly.

One thing to note: when you plug in to e-tube project they define the system into road vs. mtb categories, and the category is, I believe, determined by your rear derailleur. My Strada is a mountain bike to Shimano. Which of course makes no sense.