### 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)

_THREAD_SAFE_METHOD_
	if (p_value.get_type() == Variant::NIL) {
		props.erase(p_name);
		if (p_name.operator String().begins_with("autoload/")) {
			String node_name = p_name.operator String().split("/")[1];
			if (autoloads.has(node_name)) {
				remove_autoload(node_name);
			}
		}
	} else {
		if (p_name == CoreStringNames::get_singleton()->_custom_features) {
			Vector<String> custom_feature_array = String(p_value).split(",");
			for (int i = 0; i < custom_feature_array.size(); i++) {
				custom_features.insert(custom_feature_array[i]);
			}
			return true;
		}
		{ 
			int dot = p_name.operator String().find(".");
			if (dot != -1) {
				Vector<String> s = p_name.operator String().split(".");
				for (int i = 1; i < s.size(); i++) {
					String feature = s[i].strip_edges();