Thanks for the thorough response The Red Queen!
I'll write up a bug report soon as well then, possibly referring to this thread if the form allows that.
Hopefully this will make it into a patch of sorts then. The issues raised here are definitely not game-breaking mechanical bugs, but as you say they are minor tweaks and I'll keep my fingers crossed that these "easy" adjustments of fixing dialogue flags fit within the limited remaining development time. The alternative would be something like community patches with modding becoming more accessible now I guess, but other than bringing attention to issues I don't have the know-how to make these kinds of adjustments myself unfortunately.