### 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)
return singleton;
}
String ProjectSettings::get_project_data_dir_name() const {
	return project_data_dir_name;
}
String ProjectSettings::get_project_data_path() const {
	return "res://" + get_project_data_dir_name();
}
String ProjectSettings::get_resource_path() const {
	return resource_path;
}
String ProjectSettings::get_safe_project_name() const {
	String safe_name = OS::get_singleton()->get_safe_dir_name(get("application/config/name"));
	if (safe_name.is_empty()) {
		safe_name = "UnnamedProject";
	}
	return safe_name;
}
String ProjectSettings::get_imported_files_path() const {
	return get_project_data_path().path_join("imported");
}
#ifdef TOOLS_ENABLED
const PackedStringArray ProjectSettings::get_required_features() {