You know, I think the Fuji issue is more fundamental as it seems to relate to demosaicing the raw data from the very different xtrans sensor. Aren't you really talking about colour rendering, which can usually be resolved by Camera Calibration?
Am I talking about colour rendering? Possibly.
But could I please ask you to consider things from a different angle? Just to get something clear on my head and, hopefully, to help others.
X-Trans is a type of CMOS sensor with a Bayer filter as the OP mentioned. It uses an irregular pattern of pixels to reduce moire without needing an anti-aliasing filter. Apparently this arrangement is similar to Silver Halide film. It basically uses a 6x6 repeating pattern that goes like
GBG|GRG
RGR|BGB
GBG|GRG
-----------
GRG|GBG
BGB|RGR
GRG|GBG
So I am expecting a RAW file to contain similar data to the RAW file I get for my Nikon D600 or the RAW file coming from a Canon EOS 5D Mark III. In a nutshell:
- A short file header containing the byte-ordering, a file identifier and offset into the sensor image data
- Metadata from the camera sensor, including the size of the sensor, the attributes of the colour filter array and its colour profile
- The sensor image data (which is the RAW data) - this is going to contain readings for the red, green, blue and (second) green filters of the colour filter array
AFIK Lr discards most of the camera sensor metadata and this is a problem with certain settings available with the X-Trans sensor, such the various DR modes. I would not be too surprise if it does something similar with the Nikon Expeed 3 sensor.
If you look at the examples attached to those 2 threads, you are looking at completely different interpretations of the RAW data. It cannot be just demosaicing, there are significant colour changes. The colours look too different, just look at the greens.
The point I am trying to make is that Adobe appears to have made an attempt to shoehorn all sensors and all raw files into one single standard, the "Adobe Standard" which is the DNG profile Lr uses by default to tone map and make decisions about which colours to render. I don't have a problem with that as long as the side effect is clearly stated but the side effect is not clearly stated.
What is the side effect? Lr might not produce a "correct"/"true" reproduction of what the camera took (please note the quotes) and that in order to get a "correct"/"true" reproduction a different or custom DNG profile might be needed. Once that side effect is clear, Lr is a smashing product.
Just imagine for a minute photography reduced to Ektachrome film and/or Ektachrome film processing. The closest thing we have nowadays to different types of film are different types of sensors.