Regarding file extension issue, the problem may well originate here with my Qnap RAID server. Seems PM will do a batch rename fine on both my Macbook Pro and single external drives, but will only rename the RAW files on my RAID server, leaving me with a slew of orphaned .xmp, .thm and .xip files that retain the original camera file names. As mentioned, my workflow involves ingest to server/sort by capture time/rename.
I also think the redundant xmp/XMP files are the result of the Qnap server. Similar files have different modified dates and I suspect this is because the Qnap server is formatted to be case sensitive (a result of wanting to make it accessible to XP/Mac systems here). If you have other ideas, I'm all ears.
~ craig