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The directory structure of what ifuse is showing is what is actually stored on the device's storage in /private/var/mobile/Media (via AFC service). I guess that nautilus is using PTP or some other interface, since it has directories like 201212* which are not in DCIM format. Check gvfs-mount to see what extension it might be using.
I found that ifuse doesn't expose "live" photos shoot in HEIF format. I'm using Ubuntu 22.04 and iPhone 12.
This is a discrepency between the nautilus integration and ifuse:
For comparison, I've included the same iphone storage device as exposed in nautilus, and in ifuse:
ifuse.txt
nautilus.txt
For example, IMG_7126
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