### Godot version

v4.0.beta10.official [d0398f62f]

### System information

Windows 11

### Issue description

Using a custom "Project Settings Override" file causes Godot to immediately modify main project file (`.godot`) on startup.

The attached project demonstrates this issue. The project has the following 3 things defined:

1. Window display mode is set to "Exclusive Fullscreen" (`window/size/mode=4`) in main project file.
2. Custom project override file is set to "res://override.cfg" (`config/project_settings_override`).
3. Inside "res://override.cfg" window display mode is set to "Windowed" (`window/size/mode=0`).

Opening this project will immediately modify main project file to have "Windowed" display mode (discarding original "Exclusive Fullscreen" setting).

### Steps to reproduce

1. Open example project.
2. Go to Project Settings -> Display -> Window -> Mode.
3. Expected option is "Exclusive Fullscreen", actual result is "Windowed".

### Minimal reproduction project

[override-issue.zip](https://github.com/godotengine/godot/files/10312624/override-issue.zip)

if (FileAccess::exists(get_resource_path().path_join(get_safe_project_name() + ".csproj"))) {
		
		if (!project_features.has("C#")) {
			project_features.append("C#");
		}
	} else {
		
		if (project_features.has("C#")) {
			project_features.remove_at(project_features.find("C#"));
		}
	}
	project_features = _trim_to_supported_features(project_features);
	set_setting("application/config/features", project_features);
#endif 
	RBSet<_VCSort> vclist;
	if (p_merge_with_current) {
		for (const KeyValue<StringName, VariantContainer> &G : props) {
			const VariantContainer *v = &G.value;
			if (v->hide_from_editor) {
				continue;
			}
			if (p_custom.has(G.key)) {
				continue;
			}
			_VCSort vc;
			vc.name = G.key; 
			vc.order = v->order;
			vc.type = v->variant.get_type();
			vc.flags = PROPERTY_USAGE_EDITOR | PROPERTY_USAGE_STORAGE;