Further to all of the earlier discussion, I just upgraded to Sierra and encountered the same problems: tried to open an MPEG-2 file in MPEG Streamclip, and was told the QuickTime MPEG-2 Playback Component wasn't installed, even though it had been working fine for me in El Capitan before the upgrade to Sierra.
However, I tried using the 'Utility MPEG2 Component M. Lion.app' distributed with the MPEG Streamclip 1.9.3b8 package, and this (in combination with the QuickTimeMPEG2.dmg file from when I originally purchased the MPEG-2 codec from Apple) successfully restored MPEG-2 functionality for MPEG Streamclip -- working just as it was in El Capitan.
So, in case anybody was unsure, this technique definitely still works in Sierra, provided you have retained the original QuickTimeMPEG2.dmg file.
As for the misplaced/wrongly-displayed playback controls in MPEG Streamclip generally, my experience has been that this is only a problem on Retina screens, for what it's worth. On my non-Retina display, the controls are placed and work normally.
I hope this helps somebody looking for the answers, like I was!
David