The argument that consciousness suddenly arises due to a particular configuration of atoms is also suspect; all forms of consciousness we routinely accept are fairly robust to many configuration changes. It seems to me that consciousness hinges on the discussion of degree or content, not on the material form. A soup of atoms certainly could be aware, but not aware of in the same way that "I" am aware.
It comes down to which axioms you take. If you assume materialism is true, then your consciousness is evidence that a soup of atoms can be aware precisely the way you are. The only question becomes how that is the case.
It is only when you assume that your consciousness cannot fit within materialism that you must start looking for the alternative.
Not true at all - consciousness appears to rely on an extremely limited set of configurations, relative to all possible.