I have loaded multiple designs/checkpoints and will be processing them at the same time.
The log output has interleaved messages for the different checkpoints being processed. Is there a way to separate the log file outputs?
No, the log file echo the messages that are occurring within the Vivado process. This is true whether there is one or multiple checkpoints of a design loaded.
If a separate log is required, you should launch multiple instances of the Vivado application in order to process the different checkpoints.