ExFat -- I've had it in the format the entire time I've had PM. I've been using it on both the iMac and MacBook Pro.
I don't know why the Navigator wouldn't show all of your folders. However, ExFat, FAT, and FAT32 are Windows file systems and are not native macOS file systems.
For a problem like this, I suggest contacting our support folks at:
By email: support@camerabits.com
By phone: +1 503.547.2800 option 2
Hours: Mon-Fri, 9:00am-5:00pm [PST/PDT]
They should be able to troubleshoot the issue further with you.
-Kirk