You are not supposed to edit files from packages on classic Linux distros, that will just lead to a mess. The immutable nature of Nix store prevents you from doing that, which makes tinkering a bit harder but at least it removes the temptation.
You could still override the gsettings-desktop-schemas package when building your system but that would end up rebuilding every package that depends on it, which is everything depending on GTK. Or you can replace transplant your overridden package with system.replaceRuntimeDependencies NixOS option to avoid the rebuilds but that is ugly hack.
But since the GDM display manager responsible for the login screen runs as a separate gdm user, configuring its settings is a bit complicated.
There are actually two proper options for changing the settings as a user:
Updating dconf database.
This is what ends up happening when you change the settings in GNOME Settings.
Typically, each user has their own dconf database inside their home directory (~/.config/dconf/user).
But gdm’s home directory is /run/gdm which will not persist when system is shut down so you cannot just copy the database there.
You could create a systemd service that would populate the dconf database each time gdm user logs in. This is actually what home-manager does so you might want to use it.
If it works for the login screen, I would expect it to do so for the user as well. What specifically have you tried?
I have assumed that it changes the scaling-factor key of org/gnome/desktop/interface schema but it looks like the scaling is per display in the Settings app so it might actually do something else.
I do not have a HiDPI screen so I am not sure. Try running dconf watch / command and then try to change it in the Settings app.
Possibly it changes the scaling factor in ~/.config/monitors.xml, while the scaling-factor GSettings setting is just the default. Maybe try deleting ~/.config/monitors.xml and re log in.
Or you could copy the monitors.xml into your profile configuration and let home-manager manage it declaratively:
NixOS is not magic, it just automates what on different distros is often imperatively managed. So just like there, if you change a dconf database, it will not have an effect on completely unrelated file.
Also nixos-rebuild does not manage your home directory. You can use home-manager as a NixOS module and then it can modify the content of your home directory as a part of an activation script but that is opt-in on per-feature basis – you probably would not like it if it suddenly started overwriting random files in your home directory.