Summary: Internet Explorer 11 had flawless performance. Easily outperformed Chrome. I recommend it for all of your 60fps youtube watching :)
"As for posting, please describe what difference do you see between full fps encodes and deblinked ones."
All programs closed. No other moving images. Windows 8.1 x64. Chrome 39.0.2171.95 m. IE 11.0.9600.17239. MPC-HC x64 1.7.7. VLC 2.1.5.
Source (60 fps lossless emulator dump):
Samus' sprite alternates between transparent and solid while taking damage. Door transitions rarely have hitches. Very rarely in VLC. MPC-HC performed worse.
Super Metroid Full FPS (Chrome):
Samus' sprite alternates between transparent and solid while taking damage. Door transitions sometimes have 1-4 hitches. It is different each time. This can happen at 720p or 1080p, theater mode or fullscreen.
Super Metroid Full FPS (IE11):
Default IE in Windows 8.1 can play 60fps youtube. Visit
https://www.youtube.com/html5 . I didn't have a single frame drop during door transitions. Resolution or window size did not matter.
Super Metroid deblinked: Samus' sprite stays translucent while taking damage. Door transitions are consistently rough.