I agree with your points OP. I think over the long term, the primary place of human habitation is going to be in orbital habitats (particularly O'Neill cylinders). However, Callisto is as you say one of the strongest candidates for a place for human habitation in the solar system - if not the strongest.

Callisto as the primary hub of the Jovian system seems like the most likely outcome. I think over the medium to long term, the Jovian system becomes the largest economy in the solar system - exporting tons of raw resources to other settlements across both the inner and outer solar system. It will likely get overtaken by Neptune eventually, but Callisto as THE economic juggernaut of the solar system for a period at least is not at all far fetched.