The 2 stops of ISO performance has always been quoted as JPEG, I thought that was pretty transparent by this point. I hope that people's expectations for the 1D-X's low noise aren't too high, really. For argument's sake, let's say the 1D-X offers a 1 - 1.5 stop improvement in raw file
the 1D Mark IV. According to DxOMark, the 5D Mark II is 0.5 stops better than the 1D Mark IV for noise - therefore, 5D Mark II shooters would notice approximately a 0.5 - 1 stop improvement in raw file noise when upgrading to the 1D-X.
Of course, I plucked the '1 - 1.5 stop' idea out of the air; it could equally be a 2/3 stop improvement; we have little idea. But if you're a current model full-frame user upgrading to the 1D-X, my guess is you would be lucky to have a full stop of raw ISO improvement
Personally, I'm a 7D shooter. I find myself resorting to flash more often than I would like during indoor events, which is undesireable for several reasons. I am expecting a full 2-stops of RAW ISO improvement.