If I got it right, the problem happens on Ubuntu from nautilus (or whatever file
browser GUI) using fuse, but not as root using mount (mount.ntfs ntfs-3g).
A workaround could thus be to declare this mount in /etc/fstab on Ubuntu (and also
on Fedora for homogeneity). Making this mount automount only would be better since I
guess that this filesystem is not used often. Do not use /media for the mountpoint
since its usage should be restricted to the GUI.
Add thus for example to /etc/fstab:
/dev/sda3 /E ntfs defaults,x-systemd.automount 0 0
Then reboot or execute as root:
systemctl daemon-reload # Make systemd re-read /etc/fstab
systemctl start E.automount
Verify that the mount works, from the GUI on /Eor with: ls /E
findmnt /E should then gives something like:
findmnt /E
TARGET SOURCE FSTYPE OPTIONS
/E systemd-1 autofs rw,[...]
/E /dev/sda3 ntfs rw,[...]
The defaults options should allow everybody full read, write, execution and
directory browsing permissions (at least on Fedora). See: man ntfs-3g