### 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)

Error err;
	Ref<FileAccess> file = FileAccess::open(p_file, FileAccess::WRITE, &err);
	ERR_FAIL_COND_V_MSG(err != OK, err, "Couldn't save project.godot - " + p_file + ".");
	file->store_line("; Engine configuration file.");
	file->store_line("; It's best edited using the editor UI and not directly,");
	file->store_line("; since the parameters that go here are not all obvious.");
	file->store_line(";");
	file->store_line("; Format:");
	file->store_line(";   [section] ; section goes between []");
	file->store_line(";   param=value ; assign values to parameters");
	file->store_line("");
	file->store_string("config_version=" + itos(CONFIG_VERSION) + "\n");
	if (!p_custom_features.is_empty()) {
		file->store_string("custom_features=\"" + p_custom_features + "\"\n");
	}
	file->store_string("\n");
	for (const KeyValue<String, List<String>> &E : p_props) {
		if (E.key != p_props.begin()->key) {
			file->store_string("\n");
		}
		if (!E.key.is_empty()) {
			file->store_string("[" + E.key + "]\n\n");
		}
		for (const String &F : E.value) {
			String key = F;
			if (!E.key.is_empty()) {
				key = E.key + "/" + key;
			}
			Variant value;
			if (p_custom.has(key)) {