Those look more like debug messages than error messages, is that possible? What happens if you turn off debug log messages, republish the workspace and re-run it?
There's notably a section about some important points regarding the installation of ArcGIS Pro.
That said, please note: FME Server requires that ArcGIS Enterprise or ArcGIS Server software be installed. While it is technically possible for FME Server to use ArcGIS Pro, we have been informed by Esri Inc. that the use of ArcGIS Desktop or ArcGIS Pro in a server context violates Esri's license terms.