It came to my mind that if the photos were already organized into subfolders at the source location of Rsync command, we could leave that as it is at the target and keep maintaining identical copies.
That way, we can still upload via Rsync without getting duplicates (That won't work if I want the photos organised at my target location, but they're all in one folder on the Jolla.).

I'm hoping that at some point the Jolla camera settings will include the option to automatically store all photos in subfolders by month.
However, until Jolla does make something of the kind, I guess we can still make it work with the tools at hand.

Surely there is a command (available on SailfishOS) that we could put together including some smart placeholders so that it'll always work with new files, moving everything into subfolders, one for each month?

As you surely understand by now, I don't have the skill to do that, so maybe some of the pros here can lend a hand?