I don't konw if this may help for the ones who will try to fix this, but:
Since it works in command line, and there are strictly no errors in dmesg, since the device is properly mounted and writable in CLI, it's not a low level issue.
Since the issue is not really desktop dependent meaning that it happens in different ones (mate, xfce, cinamon, gnome), I suspect a messaging issue between mount events and the xsession itsself (dbus? I'm no expert).
It really looks like the GUI's file manager receives wrong permissions by some notification process (deamon) and does not check the real file permissions.
I don't konw if this may help for the ones who will try to fix this, but:
Since it works in command line, and there are strictly no errors in dmesg, since the device is properly mounted and writable in CLI, it's not a low level issue.
Since the issue is not really desktop dependent meaning that it happens in different ones (mate, xfce, cinamon, gnome), I suspect a messaging issue between mount events and the xsession itsself (dbus? I'm no expert).
It really looks like the GUI's file manager receives wrong permissions by some notification process (deamon) and does not check the real file permissions.