Hi, Apologies if I'm misunderstanding your issue. But from what you've posted, PM is functioning correctly if you have a RAW file, as in your example .cr2 and JPG with the same name PM will combine them if you don't want to happen; you can turn this behaviour off in settings.
As far as I know, if you have a RAW file and a JPG with the same name PM will combine them. The JPG could have been made at the same time in camera as the RAW, or it could have been made at a later date on the computer. So 'content +size+creation date+Camera' will not affect whether it's combined or not.
From what you have shown, you haven't renamed your file, and as cameras reset their numbering, they get to 9,999 back to zero, I would have thought this could cause you a problem when sorting by file name.
Personally, I would advise people to rename their images after culling, so they have a unique name. I rename my image: job-ddmmyyyy-seqn.