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Can I have separate isolated users for each SharePoint Site Collection?

No, Microsoft SharePoint user management scope is a SharePoint Web Application not a SharePoint Site Collection. It means that all site collections in a web application share same user and Site Collection Administrators can view the list of other site collection users of the same SharePoint Web Application. It is SharePoint design architecture. 

 However,  you can limit "DirectoryAccess" to "none" so Site Collection administrators would not be able to see the list of users. By the way, SharePoint Live Authentication is a trusted identity provider for Microsoft SharePoint and Microsoft SharePoint user management scope is Web Application.