After several days trying to deploy the templates, I finally did it with another method.
I followed this guide:
I made the registry changes in user config so I didn't have to use loopback processing or computer configuration at all.
I also created 2 items for each configuration because there are both English and Greek office installations in the company and the configuration in English could not copy the files to the directory written i Greek.
So now I have 2 GPO, one for word and one for powerpoint but now I encountered another issue:
Powerpoint app does not retrieve the template files as word app does.
Default personal templates location is empty in powerpoint options whereas it is set by default in word options.
Furthermore, I can see the reg key for word but not for powerpoint.
Why is this happening?
Second issue I also encountered is that when I delete a file from the source location and the run gpudate, the file is not deleted from the destination, too.
I changed action from "update" to "replace" but nothing changed, the file was still in destination.
I don't understand what is wrong here.