Just adding to the thread to include some more troubleshooting I have tried in regards to this issue. I am still having graphical glitches on startup/restarting my 2015 rMBP running macOS Sierra 10.12.1 connected via HDMI to HDMI to an external Acer 1080p monitor.
The issue is the Apple logo and progress bar on startup/restarting is momentarily being shrunk and shifted to the top left of the screen both on the laptop itself and the external monitor. Everything is fine from the login screen onwards since 10.12.1. This issue does not happen when using the rMBP without an external monitor.
I have tried both PRAM and SMC resets which unfortunately did not help with the issue. I have also booted into recovery and ran first aid on my internal SSD. I have also tried different HDMI cables and using a Thunderbolt to HDMI adapter from the rMBP into different ports on the external monitor.
I'm not really sure what else to try, I have never had this problem with the exact same hardware setup running on OS X El Capitan 10.11. I read that 10.12.2 is on the way and has begun beta testing, I hope that will include a fix.
Has anyone had any luck?