I don't use GNOME, but...

The whole 'directory'/'folder' concept is just shit all around. It's a bad
abstraction and never really made sense. It was designed by Xerox as part
of a basic GUI to run a printer, FFS.

But it's one we are stuck with.

Folders make sense in Gnome because not everything you see as a folder is
really a directory on your file system. You have your 'fonts' folder. It
corrisponds with stuff that goes on in ~/.fonts, but only loosely. Same
things with folders when your using 'smb://' to view windows servers or
whatever.

There are all sorts of little things like that. It is really very bad and
makes things more confusing unless you happen to have a good understanding
of what is happening in a OS, but it mostly works as long as users don't
think about things too deeply.

You can thank Microsoft and Apple for this.