The "Copy Settings" button in the region panel calls the "SetX11Keyboard" dbus method (implemented by systemd-localed) and passes everything as layout instead of properly distinct between layout and variant; resulting into a config file that X cannot parse:

-----
g_dbus_proxy_call (localed_proxy,
                           "SetX11Keyboard",
                           g_variant_new ("(ssssbb)", layout, "", "", "", TRUE,
TRUE),
                           G_DBUS_CALL_FLAGS_NONE,
                           -1, NULL, NULL, NULL);
-----

As specific example "de nodeadkeys" will get passed as layout while only "de" is the layout and "nodeadkeys" is the variant:

------
<method name="SetX11Keyboard">
    <arg name="layout" type="s" direction="in"/>
    <arg name="model" type="s" direction="in"/>
    <arg name="variant" type="s" direction="in"/>
    <arg name="options" type="s" direction="in"/>
    <arg name="convert" type="b" direction="in"/>
    <arg name="user_interaction" type="b" direction="in"/>
</method>
------

Quoting Peter's comment from the downstream bug:

-----------
In GNOME, go to the region and language panel, select a layout with a variant
(e.g. German, nodeadkeys). Go to the System panel, click on "Copy Settings".

This causes 00-system-setup-keyboard.conf to be linked to /dev/null and a new
file 00-keyboard.conf is put in place by systemd. That file has a configuration
that cannot be read by the X server.

        Option "XkbLayout" "at nodeadkeys"

Should instead be:
Option "XkbLayout" "at"
Option "XkbVariant" "nodeadkeys"

For multiple layouts, each value must be a comma-separated list. So if your
layouts are "us,at(nodeadkeys)", the two options must be

Option "XkbLayout" "us,at"
Option "XkbVariant" ",nodeadkeys"

Note the comma before nodeadkeys, otherwise it's assigned to the first layout
(and us(nodeadkeys) doesn't exist).
---------