Esp in comparison to your Star Trek analogy, maybe the issue (as it often is for me) is whether the fantastic is something added on to the world, or a rearrangement of what you consider the baseline reality. It's one thing to say "Star trek adds transporters and warp drive to our universe, and you just have to accept those additions" and imo a very different on to say "In the star trek world a retrovirus can cause you to grow extra limbs and add up to 200 lbs of body weight, and curing that virus will magicly disolve those additions, and also humans are descended from spiders!"

In the same way "Magic can extract parts of the mind and personality and make them 'real' in a way best described as souls" could be easier to take than "The base reality of the universe is that everyone has a dualistic souled nature." Its reality plus vs reality is different.