Comment # 8 on bug 1230851 from Stefan Hundhammer

Ah, the old problem with keyboard and language settings being defined in a
dozen different locations... see also bug #1228104.

gnome-terminal as well as all the other terminal emulators (konsole,
xfce4-terminal, xterm) is not a reliable way to check the keyboard layout: The
settings done in the display manager (GDM in your case, LightDM or KDM in other
cases) can all override the system-wide settings.

The console settings in /etc/vconsole.conf only affect the real console
tty1..tty6 (or however many you may have defined).

All the GUI terminal emulators really use the X11 (or Wayland) keyboard
settings which may come initially, before your first login, from system files;
but if you ever clicked anywhere in the display manager menus or in your
desktop's settings, those will override that from now on. All the major
desktops have a "keyboard" applet somewhere in their task bar. Some of them may
have a "leave system defaults" setting, but IIRC not all of them.

That makes the whole process even more unpredictable; the first login may
behave different from subsequent ones. And if there is an existing home
directory, settings in ~/.config/...  may interfere.

This is very much as in bug #1228104 comment #2, which is about language
settings, but keyboard settings are very similar.