Wow.I just was looking for a way to customize that!
Good to know this@arnebrucksch!
Changes were made in FME Server 2017 that caused folders with the names of the writers used in the workspace to be created in the zip file returned by the data download service.However in 2018.1 we introduced another change to give back more control to help fix any unwanted behaviour.
In FME 2018.1 onwards,you can remove these unwanted folders by setting the structure of the output zip file when publishing the workspace to FME Server.
From the Register Services page,click Edit beside the Data Download service,then click the '...' button next to Include Writers in Download,then click on 'More...'.This will open a dialog that will let you set up the paths for each of the files within the zip file.