I need the cooked uncompressed files and not the original files.
SteamCMD loads the mod and creates 2 sub folders: WindowsNoEditor and LinuxNoEditor. Inside of each of them are the cooked files in a compressed format. The game (or server in this case) needs them in an uncompressed state and I have no idea how to extract them.
When you use Windows and run the Ark launcher, the tool starts steamCMD to download the mod. After that step you have them as compressed files inside steamCMD/workshop/content/360110/<modId> (360110 is the Ark app id if I remember correctly :)). The tool decompresses the files of WindowsNoEditor automatically and puts them in the content/mods/<ModId> folder of your dedicated server.
All I need is that extraction part as I already wrote in my first post.
EDIT:
After some digging, I found out that they are compressed with Ionic.Zlib. That should help other people who want to use their own tools for server management 