I understand your concerns. Regrading the virtual connections I'm currently elaborating with Tableau (partners) what is possible now and what ideas are there for the future in terms of access via 3rd party tools.
In general, as Tableau offers an Hyper API, it is up to Tableau to ensure that most of your mentioned concerns/risks are mitigated.
In our case we are more referring to what you envision for EasyMorph as a computing platform, where also the hyper files on Tableau Server are generated and updated via EasyMorph. So Tableau Server will handle data storage, data access policies (as long as there is no alternative on EM server) and is a possible entry point for self-service visualizations.