Version 1.31+ should automatically set these settings for you.
Unchecked YT Center Settings > Player > Player Size > Enable Resize.
Unchecked YT Center Settings > Player > General > Scroll to Video. YT Center will scroll to the wrong location.
Screenshots
After loading the video webpage you will see:
It appears above the rest of the site, so you can scroll down for the description, related links, etc.
Changelog
1.44 - Oct 31, 2014
Fix a second video player getting loaded when running this script along Youtube Center, this reintroduces the progressbar bug for users with YT Center. Please use the dev build of YT Center until the author pushes the fix to the main build.