the point is that if there were 3 stops less light, the noise on that same image (at 12800 ISO) would have been a bit higher.
This is so true. The visibility of noise is about the signal to noise ratio. Sports photos, in relatively bright light in comparison to a dim lit street or a dark pub interior, that have been set to high ISO for the shutter speed show much better at the same ISO speed than the shots from that low light pub or street. In both cases the right exposure is quintessential. I guess the high ISO noise resistance is for that reason better for (relatively) well lit situations. Anyway, the 1DmkIV is again a step forward in comparison to the 1dmkIII. It's in my limited experience so far about 1,5 to 2 stops better. A shot at 12.800 looks about the same as a 3200 from the 1DmkIII, which was not bad either. Will give me a little more headroom in the church or theatre, but not so much as to get overwhelmed, since the 1D(s)mkIII are for those lighting conditions already very satisfying to my taste. I guess it's the sportsphotographers and street photojournalists that will like the new high ISO treatment best. They can go to higher shutter speeds and/or do their reporting job without a flash more often.
Enjoy the new cam, EOSfun!