No. As long as you record in movie mode (not photo!), the exposure values will be the ones displayed by ML (not by Canon!)
Yup I always record RAW video in movie mode, I've never tried it in photo mode. It's a habit I suppose, a stupid one, since I have to rotate the mode dial all the way around (I'm using 60D)
By the way, does Auto ETTR work when the screen is off? With RAW video now being able to record with the screen off, it is highly unlikely that one would leave the screen on if they are shooting a time lapse video. Does everything continue running in the background even if the screen is off? What happens if global draw off is set in powersave options?
Edit: Even though Auto ETTR seems to say that it works in video mode as long as you shoot RAW video, but it doesn't seem to work (it doesn't change any exposure parameters despite me intentionally setting parameters that underexpose the image). It sometimes seem to change the ISO, but it somehow quickly changes back to what I had set earlier, resulting in the original underexposed image. It sometimes also say VSync err.
Edit 2: After further testing, I found that the Auto ETTR errors are related to using FPS override. When FPS override is used (at least with the FPSes that I tested), Auto ETTR will not work, and it will show a VSync error.
Edit 3: Upon even further testing, Auto ETTR does work even with FPS override (it still shows the VSync error), but the live view image never shows the actual image nor does it appear to change any image parameters, but the video is of correct exposure.