Could it be that automerge is not working because you are missing a hyphen? The movie section in the Jellyfin docs states:

To distinguish between versions, each filename needs to have a space, hyphen, space, and then a label.

https://jellyfin.org/docs/general/server/media/movies

Jeff Geerling ran some benchmarks on USB storage options in 2020, including a pen drive SSD: https://www.jeffgeerling.com/blog/2020/fastest-usb-storage-options-raspberry-pi

I also use those, but (shame on me) I’ve never tested the backups. Have you ever restored such an image backup?