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It seems to me that hypotheses about a creator are of the "filling the gaps" kind whereas string theory and the multiverse are extrapolations of scientific theories.

It's analogy time! Let's consider a computerized virtual reality universe inhabited by digital beings that have achieved intelligence comparable to ours. They are investigating the nature of their reality in the same way we study ours and they find that their universe can be described in terms of bits of information that interact according to mathematical logic. They observe that their universe obeys programming rules that appear arbitrarily set to be compatible with intelligence and that it had a beginning, appearing suddenly from seeming nothing. When they try to extrapolate what might have occurred before that beginning, perhaps they also come up with something similar to a multiverse concept. It seems to me that these digital beings would be completely justified in considering the possibility of an intelligent creator of their universe, particularly since in their case, that would be the correct assumption.

Is our situation so different? Why is the consideration of an intelligent origin of our universe now an inappropriate appeal to the supernatural?

Our experience of intelligence and sentience is that they arise from a certain type of complexity. Nothing supernatural about that. Not sure why assuming the origin of the universe is simple is consistent with science, but assuming a complex origin is not.
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