when i mount a disk somewhere in my home directory (configured in /etc/fstab) then Nautilus show a little icon in the top right corner of folder icon to indicate that directory is a mounted directory. Good idea, i like it!
But not when i mount it to somewhere else, e.g. /mnt.
With the disclaimer that I use neither GNOME nor its Nautilus file manager, the behavior you describe would indeed be perfectly logical and consistent.
If the device is listed in /etc/fstab — which means that it’s got a defined mountpoint — it is considered a regular part of the filesystem hierarchy, even if the device is not permanently mounted.
On the other hand, when you manually mount the device to some random directory that’s not listed in /etc/fstab, then the system no longer recognizes the mounted filesystem as part of the regular filesystem hierarchy, and therefore, it regards the mount as unfamiliar and random — which it is, of course.