Well the Nvidia web driver came out for my GTX 980 (yes it works again!) and suddenly 3440x1440 started working. GT120 which uses standard OS X drivers IS NOT working. Looks like a 3rd party fixed it before Apple did.
The new 10.12.1 update resolved it for me. My rMBP 15 connected to a Benq 1440p monitor is now correctly identifying and connecting as 2560x1440@60Hz over HDMI as it did with 10.11.
Well the Nvidia web driver came out for my GTX 980 (yes it works again!) and suddenly 3440x1440 started working. GT120 which uses standard OS X drivers IS NOT working. Looks like a 3rd party fixed it before Apple did.