I'm not sure if this is new in 1.3 or because of a finishedTrigger in 1.3, but let me explain.

Reproducibly, I have an incomplete log file at /Library/Logs/Setup Manager.log. It's around 12Kb in size and stops in the middle of a log message. (I am happy to provide an example file privately.)

Perhaps relevant to 1.3, I am testing a finishedTrigger that installs Jamf Connect and restarts. It's possible that either the Jamf Connect install kills the loginwidow and Setup Manager processes is doing so before the log file is written to disk or the shutdown command is cancelling a deferred write.