The ISO setting alone doesn't have to change much, but it might (depending on ADC gain amplification). Underexposing will change everything (due to Poisson distribution statistics), regardless of the sensor.
This sort of confusion would be avoided if we stopped using "ISO" to mean so many related but different things. Erik is clearly talking about reducing exposure level and giving the sensor less light, and thus when he says "high ISO", he means high
Exposure Index, one of the numerous quantities defined in ISO standards. Exposure Index, is, by the way, the main intended significance of the "ISO" setting on digital camera, through effects like adjusting the shutter speed and aperture combination chosen in auto-exposure modes and doing default raw-to-JPEG conversions on the assumption that exposure levels are lower when a higher ISO exposure index setting is used.
But some people insist on assuming that measures like the saturation-based base-ISO sensitivity, a measure of highlight headroom in the sensor or raw files, are or should be what the ISO dial on a camera specifies. By the way, the traditional ISO measure of film speed is distinctly different from either of these two: it is a measure of how high the exposure index can go (how little exposure the film can be given) while still meeting some standard for image quality in the shadows. The closest counterparts for digital photography are the rarely-used noise based SNR10 and SNR40 standards, which are the exposure index levels at which mid-tone SNR levels are 10:1 and 40:1 respectively.
Anyway, the bottom line is that Erik's figure of about 125 photons at mid-tones when exposing at an exposure index of 6400 limits the SNR to about 11:1 no matter how low the sensor's internal noise levels are. This is just better than the SNR10 standard, traditionally described as a barely acceptable mid-tone SNR level (while 40:1 in the mid-tones is traditionally described as "excellent").
So to restate Erik's conclusion in something closer to the language of the ISO standards: for a sensor with full well capacity of 40,000 and saturation-based "base-ISO" sensitivity of 100, an exposure index of 6400 gives a mid-tone SNR of at best about 11:1, so the more generous noise-based SNR10 sensitivity is at best just slightly more than 6400. Perhaps Phase One has chosen its maximum exposure index setting of 6400 based on this being near the SNR10 limit.
Aside: for the more cautious SNR40 mid-tone noise standard, a mid-tone signal of at least 1600 is needed, and in Erik's case of exposure at EI 100 giving about a 8000 mid-tone signal, this would give a SNR40 sensitivity of only about 500! That EI level is about where people seeking excellent IQ and very fine tonal gradations still need to be operating, and it is determined almost entirely by photon shot noise and photons counts, not by the sensor's noise floor, so the new Sony sensor will not change that situation much.