I just joined this forum in order to share what I learned about this problem, in my case at least. I have a 2020 Cannondale Supersix. The only way it shifted properly was to have the Di2 rear deraileur adjustment all the way to the outboard side (+16 clicks). Even though it shifted fine like that, it bothered me because if something needed adjustment on the road, I might be out of luck.
After reading all I could find about this problem, I added a washer between the hanger and the deraileur, as others have suggested. It didn't buy me much, if anything. I then tried bending the deraileur hanger (removed from the bike and placed in a vice). I hit it with a plastic, sand filled hammer to try and bend it. Even though it would seem like I moved it a bit, after I put it back on the bike, it I didn't bend it at all. I tried this several times with the same result. That deraileur hanger is surprising rigid. Obviously I could hit it hard enough to eventually bend it, but I wasn't sure that was the best thing to do.
I kept examining and thinking about the problem and eventually realized something: the part of the bike frame that the deraileur hanger mounts to was actually just slightly angled inward. It is extremely subtle and hard to see, but it is slightly angled and not entirely vertical.
So, I meticulously cut a shim out of thin aluminum to place between the frame and the hanger. I cut it carefully so that it matches the outline of the hanger. Then I sanded the shim on an angle to make up for the incorrect angle of the mating surface of the bike frame. Assembled, the upper limit of the shim is thinner than the lower limit of the shim. This negated the slight angle of the bike frame mounting surface. Hope this make sense.
After reassembly and and adjustment I was able to electronically adjust the Di2 rear deraileur 5 or 6 clicks inboard! I had solved the problem. I was always dubious that the issue would be on shimano's end, and I was correct. The problem was with the bike frame.
Hope this helps some folks. If my description is clear as mud, please reach out and I'll try to explain better or maybe post some pics.
Last edited by Bspang; 08-03-21 at 08:43 AM.