I don't know specifically about the 1D3, but with most (all?) cameras, shooting in the extended ranges or with highlight tone priority enabled will reduce image quality.
With highlight tone priority, what the camera does is under-expose the image by a stop, and then increase it in software with a curve that preserves highlight tones. So ISO 200 with HTP is actually ISO 100 pushed a stop, increasing noise and lowering the amount of detail captured in the shadows.
If your camera's base ISO is 100 and you enable the extended range and shoot at 50, the camera is simply shooting at ISO100 and under-exposing by a stop. So you don't gain any quality, and are losing a stop of information.
If your camera's max ISO is 3200 and you shoot at 6400, it's actually shooting 3200 but over-exposing it by a stop, again, no quality improvement and you lose a stop of information.
In some cameras, I think even in the normal range, shooting above ISO 1600 can have the same effect, being a software boost rather than increasing the sensor gain.
If you're shooting JPEG, it might be useful to use highlight tone priority or the extended ISO ranges, but if you shoot RAW you're better doing it in the RAW conversion.