Publishing an offline service definition to ArcGIS Enterprise via ArcGIS Server Manager does not create a new server folder specified in the offline service definition and does not publish the map layer in the specified portal folder.
This issue is not reproducible. When a new server folder is specified during publishing in ArcGIS Server Manager, the service is correctly placed inside of the new server folder. As for the new portal folder, it is not possible to specify a portal folder when publishing via ArcGIS Server Manager.