I have the article on the SS Suveric and it's docking at the pier in Seattle as well as the Portuguese Consul's description of the voyage. It does not mention Sao Miguel or St. Michael's in either of these articles. I have the manifest of passengers from Portuguese Immigrants to Hawaii by E. Knowlton as well (which I never noticed mentioned them either). If you have a different list, I would love to see it.
Since there is no passport record in Madeira for my great-grandparents, it is possible that they acquired one in the Azores. They wouldn't need a passport to get from Madeira to Sao Miguel as they are both Portuguese regions.
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. I would love to see what you have with the Azores info on it.