Per Publish Hyper Files it appears that publishing Hyper extracts with multiple tables cannot be done programmatically. I think this degrades the user experience and has come up as an issue for the open source projects in the Tableau ecosystem like this:
Hoping that this restriction can be lifted easily!
--> Community Manager update [Ciara Brennan]
Marked as Duplicate
Please refer to https://community.tableau.com/ideas/10308