GNOME Settings daemon only uses xkb config for initial setting of input settings. What is worse, those settings cannot be easily updated in NixOS configuration (nixos/dconf: Allow creating custom databases · Issue #54150 · NixOS/nixpkgs · GitHub), you will have to reset corresponding dconf keys (and maybe re-login) for the config to be read. See also Problem with `xkbOptions` - it doesn't seem to take effect