Hi Umberto,
Just wanted to add that I too have experienced this problem with the update feature of the Couatl engine within Prepar3D.
Although recently I have used a migrator tool, this problem existed long before I ever used it. My registry keys for P3D had not been touched when the same message came up that the program can run only from the Couatl root folder. I have never been able to successively use the "update" feature within P3D since it was created. I have always installed using all the default locations, other than P3D which resides on a separate drive. I have avoided tinkering with any registry info to ensure I do not create future problems with any add-on content.
The only method I have been able to use is to download the Add-on manager from the site and run the installer, then all works fine. Within Prepar3D, I get the error message about the root folder.
I also get the same error when I navigate and execute the Update.exe within the Couatl folder of FSdreamteam within the Prepar3D folder, (P3D not running).