I am also experiencing this problem in my brand new MacBook pro early 2015 running MacOS sierra 10.12.1. I have not changed the default settings of display.
I can confirm that this problem has not been corrected and the flickering is happening with both Safari and Chrome. I cannot check Firefox, because I have not installed Firefox in my mac. At first, I freaked out and I thought that there was a hardware problem, but I am relieved now that this is probably due to an error in the drivers of the video card.
Apple, please fix it!
PS1: I am running Netflix in HD, if this is of any use.
PS2: The flickering can be appreciated better, if you watch Netflix in full-screen in a dark room, when dark scenes are on display. Sometimes, it's subtle, but existent and annoying. I prefer not watching in fullscreen than seeing this flickering.