Ruben I'm only a junior Tableau Server Administrator, but it sounds to me like you're going the long way around for a security solution that may already exist in the software. But to answer your first question:
The question is during the refresh of a workbook that's using an unpublished TDE, is the server pulling the data from the original TDE that's stored in a file folder?
Probably. I say probably because there are other factors at play. For instance if you publish a packaged workbook to the Server, then it would NOT be refreshing from the original file. Here's an excellent post about what lives where, and how it is refreshed:
Finally, I think you'll get more specific help if you move this over to the Server Admin Community: