I found another iteration of this bug (and others). Using Microsoft Remote Desktop for Mac on a MBPr connecting to a Windows 10 PC. Previously on both Yosemite and El Capitain I had each Display as a Separate Space and would connect in full screen. I have three external monitors and Microsoft RDP would be full screen on all four (including the MBPr screen). Each display had it's own space so I could swipe left/right with 3 (or 4) fingers to swap between my native OSX/macOS.
This functionality was amazing. It was much better than running Fusion, more seamless, faster response, everything was amazing. Was.
Unfortunately, after upgrading to macOS Sierra I can no longer produce this same workflow. If I have each display in it's own space, Microsoft Remote Desktop does not recognize the other displays and only shows up on my MBPr screen (which because of Microsoft's Windows 10 Anniversary Update the resolution is skewed horribly). If I disable each display having it's own space, the swipe left/right affects the entire virtual Desktop making it all or none.
Before, I could have 3 monitors showing Windows applications and 1 showing my Mac apps, or 2 and 2, or 3 mac 1 windows, and 0/4 or 4/0, whichever I wanted, it worked. It made my life coexisting between two platforms amazing. Using Cloud Storage I was able to keep my file system in sync and it was like having one amazing super computer (the Windows PC is my lab system running VMware Workstation, has 32gb of RAM, quad proc, dual RAID1 SSD, the works.
Unfortunately I think the issue resides on both the changes to macOS Sierra (for the spaces and swipe left/right issue) and the Microsoft Anniversary update (for the skewed resolution showing up as 1440x900 as opposed to the MBPr resolution, wether scaling is enabled or disabled). I am just hoping this gets resolved sooner than later so I don't have to keep jumping through hoops to get my work done.