I looked at the issues you linked and what I am experiencing a bit more in depth. I think my problem is something different. But clearly, this is complex stuff.
I seem to get magenta highlights whenever using a white point correction sufficient to prevent extra clipping, regardless of whether HLR is on or what mode is used, so it is not 2256.
Flat-field itself works without magenta color cast (I am using a nightly build, the 5.8 stable was broken), so it is not 3361. I don’t use a dark frame, so it is not 5848 either.
I think it is just the same problem that stops you from using clip control on an already clipped photo. Color cast on already clipped highlights. So it appears there is no way around even more clipping from flat-field.