### 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)
value = p_custom[key];
			} else {
				value = get(key);
			}
			String vstr;
			VariantWriter::write_to_string(value, vstr);
			file->store_string(F.property_name_encode() + "=" + vstr + "\n");
		}
	}
	return OK;
}
Error ProjectSettings::_save_custom_bnd(const String &p_file) { 
	return save_custom(p_file);
}
Error ProjectSettings::save_custom(const String &p_path, const CustomMap &p_custom, const Vector<String> &p_custom_features, bool p_merge_with_current) {
	ERR_FAIL_COND_V_MSG(p_path.is_empty(), ERR_INVALID_PARAMETER, "Project settings save path cannot be empty.");
#ifdef TOOLS_ENABLED
	PackedStringArray project_features = get_setting("application/config/features");
	
	if (project_features.is_empty()) {
		project_features = ProjectSettings::get_required_features();
	}
	
	const String rendering_api = has_setting("rendering/renderer/rendering_method") ? (String)get_setting("rendering/renderer/rendering_method") : String();
	if (!rendering_api.is_empty()) {
		
		if (!project_features.has(rendering_api)) {
			project_features.append(rendering_api);
		}
	}