Today the 5D Mark Free software gets zebra stripes to show overexposed portions of the video. They are not recorded to the quicktime file. Eventually the threshold will be configurable and the stripes will be toggleable. The color and threshold are hardcoded right now and they can not be turned off. They don't play well with the other onscreen info displays, although one side-effect is that they erase the auto-focus and zoom square.
With the announcement from Canon that full manual control is coming, the 5D Mark Free project can start focusing on these sort of enhancements, rather than just manual exposure control.
EDIT: FAQ updated to reflect new Canon firmware and new name of project.