As far as chapters would depend if they are grouped on seperate pages, yes it can do that by printing Chapter pages seperately then re-arrange the chapters. But if they were on the same page no that can't be done.
I tested it while I was writing this reply. I would print out 1 page or group of pages to PDF Creator then click waiting. Every other print to PDF Creator would come up the same queue. After finishing it I could re-arrange to order of the pages or groups of pages then combine them.
Once you have printed a group you can't split the group though, would need to print the pages from the group seperately.
Maybe Dave's suggestion will work on groups or splitting same pages if you have Linux.
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