Yes, the updater will download a custom GSX profile for all FSDT sceneries.
However, thanks to your report, I noticed a problem with it: it downloaded the profile in the package own scenery folder and it used the %APPDATA%\virtuali\GSX\MSFS folder only if the scenery was found in the Official folder ( FSDT bought from Marketplace ). This works fine in the default GSX config with the SU10 Navdata API Disabled but, if it's Enabled, the Community folder and the .BGL won't be read anymore and so the profile in the Community folder, which means the updater should download the profile in %APPDATA% as well, since the package\scenery in the Community folder won't be read anymore in this case.
The FSDT Updater has been updated now, so it will download the profile in the %APPDATA% folder too, so it will be used even with the SU10 Navdata enabled.