Well, just got reply from Atomos about the bad pixel issue in 6.2K raw:
Please note that our engineering has gone over your case and replicated and tested your setup.
Unfortunately, the issue lies with the camera as it is outputting the bad pixel in 6.2 k RAW.
We would love to help you fix the issue but as it is on the camera end our hands are tied.
Please contact the camera manufacturer to get this issue resolved.
Fuji doesn't give a shit about my emails, so I wouldn't expect a fix anytime soon. This, and the framerate issue, and also the fact that Fuji's ProRes RAW has noticeably less dynamic range than F-Log, not to mention F-Log2, makes me loose faith in this company, they do a lot of things right but they always have to fuck up little things like this.