From *my* usability perspective (YMMV), two things bother me about the Publish to PDF pod.
1) Source document doesn't switch to the active document. So, I have document AA.fm open and publish it to PDF, but BB.pdf is created from BB.fm, because that's the file in the Source Document field and it must be manually changed, or so it seems.
2) Output folder should default to the location of the source document. So, I select AA.fm as my source document and publish it to PDF, but I can't find the file because it published in the BB.fm folder, because I hadn't manually changed that. This annoyance is worse than item 1).
3) Having to track a settings file is just bothering me. Best practice advice on this would be appreciated.
Re 1: You can set the source document to "Current". Then it will always the currently active document.
Re 2: An alternative route to the publish pod for PDF publishing is File > Save as PDF (make sure you have Update 2). This will open the save as pdf dialog and default to the location of the active document. Just hit enter and get your PDF.
Re 3: Up to your preference. I have mine in %appdata%\Adobe\FrameMaker\15 and keep a backup in the location where my FrameMaker setup.exe is 🙂