I am afraid that either the removal of color filter or the setting of RT is wrong.
Because “picture 1” above is normally seen by a camera with color filter. When the color filter removed, the sharpness and image quality are supposed to be improved.
If I mannually turn ”picture 2" into black and white. The quality seems to be better than “picture 1”.
If Fuji is doing some processing (like dark current or read noise subtraction or white balance pre-copnditioning) to their raw files, it will show up as a faint mosaic pattern on debayered camera with no demosaicing. This is a common problem with black and white modified Nikon cameras (I had one of those back in the day).