How do you create a Report Model in SQL Server Reporting Services 2016 (Native Mode)?

You cannot as it is discontinued.

RS Web Portal is the new name for Report Manager of earlier versions.

The following two features related to Report Model are discontinued  in SQL Server 2016.

Feature                                                                Replacement or workaround
Upload report models through the web portal     This can still be done through the SOAP API.
Manage report models through the web portal    This can still be done through the SOAP API.

Note: Whereas HTML4 is supported, the future SQL Server Reporting Services will be using HTML5.