I’ve actually been looking at the way the Desktop engine handles the logging for a separate reason, and I think I now understand a bit more.
When Desktop is loading the app for the project, that logging is never getting passed to SG Desktop main UI process, however it should as far as I can see, and I’ve tested, still get output to the tk-desktop.log. So that explains why you wouldn’t see it in the console, but I’m still not sure why you are not getting a message in the log file. I get an error like this:
App /Users/.../tk-multi-pythonconsole failed to initialize. It will not be loaded: ...