This reads like a sound analysis. But I fear 'fixing the plot' is out of the question at this point. What should be possible is for Larian to learn from their mistakes, for their next games. They should make damn sure that they have a good backbone for the story in place, next time. It should be good enough to withstand and enable all story branches that are added, changed and removed later on.
Nothing will change in their next game with all the simps praising BG3. What BG3 has shown is that you do not need a good story for RPGs. Just pack waifus and genital customizations in and you are done.