The Data Extract Command-Line Utility is really just a glorified way to tell Tableau Desktop to run a refresh or add data. People tend to use it in combination with Windows Scheduler to run refreshes are desired times. However, the extracts are still created within Tableau Desktop. The only mechanism we have for creating an extract via scripting would be our Tableau Data Extract API which is now a part of the SDK. You may also want to look into a third-party solution like Alteryx.
I have recently published a library to create .tde if you point it to the right view or table. It can then publish and overwrite it. I think this library may suit your needs. I initially wrote it for MSSQL but had to alter it to suit our new database EXAsol. So it needs some testing on MSSQL but I am more than happy to make the changes or accept contributions.
If you could try it and let me know of any issues using it I would much appreciate it.
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