Simplified story: One engine can only use one specific python version. So if you have 2 workspaces running - with different versions of python, they will fail giving this error:
The Workspace requires Python version 3.6, but Python version 2.7 is already loaded Workspace requiring Python 3.6 is requested to run on an FME Engine configured to use a Python 2.7 interpreter. FME cannot continue given the Python version mismatch
A fatal error has occurred. Check the logfile above for details
GUI-suggestion on FME Server:
Which will result in a warning when publishing workspaces to that server: