### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
const String res_path = resource_path.path_join("");
		
		
		cwd = cwd.path_join("");
		if (!cwd.begins_with(res_path)) {
			return p_path;
		}
		return cwd.replace_first(res_path, "res://");
	} else {
		int sep = path.rfind("/");
		if (sep == -1) {
			return "res://" + path;
		}
		String parent = path.substr(0, sep);
		String plocal = localize_path(parent);
		if (plocal.is_empty()) {
			return "";
		}
		
		if (plocal[plocal.length() - 1] == '/') {
			sep += 1;
		}
		return plocal + path.substr(sep, path.size() - sep);
	}
}
void ProjectSettings::set_initial_value(const String &p_name, const Variant &p_value) {