### 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 (!OS::get_singleton()->get_resource_dir().is_empty()) {
		
		
		resource_path = OS::get_singleton()->get_resource_dir().replace("\\", "/");
		if (!resource_path.is_empty() && resource_path[resource_path.length() - 1] == '/') {
			resource_path = resource_path.substr(0, resource_path.length() - 1); 
		}
	}
	
	if (!p_main_pack.is_empty()) {
		bool ok = _load_resource_pack(p_main_pack);
		ERR_FAIL_COND_V_MSG(!ok, ERR_CANT_OPEN, "Cannot open resource pack '" + p_main_pack + "'.");
		Error err = _load_settings_text_or_binary("res://project.godot", "res://project.binary");
		if (err == OK && !p_ignore_override) {
			
			
			_load_settings_text(p_main_pack.get_base_dir().path_join("override.cfg"));
		}
		return err;
	}
	String exec_path = OS::get_singleton()->get_executable_path();
	if (!exec_path.is_empty()) {