The noise floor is variable depending on amplification that is applied, which depends on the ISO setting. Then there is the photon collection efficiency, which Nikon may have been able to improve (according to an interview by dpreview, Nikon improved the light gathering which I take to mean the QE). I would guess what has happened is increased QE and increased read noise at base ISO (due to faster ADC and perhaps a different amplifier design where high ISO is emphasized). Also the ability to do 4K recording may have required a different design which has more noise at low ISO.
As far as I know the 1D X was very successful for Canon whereas the D4/D4S were not so much for Nikon. The AF system may have been a major difference with the extended array of cross type points in the 1D X (now Nikon has that too). Nikon got some criticism from D3S users that the D4 was not much of an improvement at high ISO (few seemed to care that Nikon improved the low ISO DR in the D4 vs. D3S). So, Nikon may have decided to do what the market seemed to ask for: optimize everything for high speed and high ISO. It is fitting that whatever they do, there are complaints online.
Suddenly there are people who
do care about the base ISO dynamic range in this type of a camera.
Well, perhaps they can now buy a D4s either used or discounted. For me I care more about the cross type AF points than a minor difference in low to mid ISO dynamic range but I do appreciate if the designers are able to make a fast camera also a good general purpose camera.
Personally, when they started increasing the base ISO dynamic range (with the D7000 and later the D800) I was sceptical of the usefulness and importance of it, but I quickly realized that the images genuinely looked better and could be edited in a more flexible way still retaining the quality. But I felt the D800 at ISO 6400 after correcting the white balance in low K lighting (candle light) produced a lot of noise in the blue channel and the images were IMO unusable (whereas the D800 at ISO 6400 in daylight was ok, since the blue channel didn't have to be amplified), so I felt there was a definite compromise. The D750 is a bit better at high ISO than the D800 (or D810) with even underexposed ISO 6400 shots being ok after increasing the curve in raw converter, but the body is a poor match for my hands (I find it very uncomfortable to use with gloves on, also it feels unbalanced with even mid sized lenses) so I look forward to what the D5 can do.