Ugh, so sad to see you post this because it has been the bane of my youtube watching with my ATV2, and I was REALLY hoping they had built in some screen control into the ATV3. I like to watch video game replays on youtube and have just had to deal with the clock being cut off along with lots of other information at the edges of the screen.
For me, I have tried everything I can think of to try and remedy this and nothing works. Shoot I would have even settled for a marginally zoomed OUT view with a thick black border on all sides but I couldn't find a way to get that either.
Personally, I have a Panasonic 46" plasma which I believe has it's edges of the actual screen covered by the plastic frame. So I think the ATV2 is displaying a complete picture but it's physically being covered up by the way my tv is constructed.
So lame ATV3 doesn't have some sort of video output control so users can acclimate to any tv.