It's not that different the way Foveon is different to the normal bayer sensors. It has a differing color filter matrix, but that only (Supposedly) aids in resolution. For ISO gains, one needs a super efficient sensor and from all records, Sony/ Nikon are doing a better job than most at it.
Remember, at the same ISO/SS/Aperture, a FF sensor collects more light than an APS-C one, given the larger surface area. At the same reproduction size, the image from the FF sensor (If it is from the same generation and has at least equal efficiency) would have less noise.
Not that any of this matters to me anyway. I've rarely ventured above ISO 3200 and prefer low ISO, tripod work these days. The D800E seems to be perfect for that.