### 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 (resource_path.is_empty() || (p_path.is_absolute_path() && !p_path.begins_with(resource_path))) {
		return p_path.simplify_path();
	}
	
	int p = p_path.find("://");
	bool found = false;
	if (p > 0) {
		found = true;
		for (int i = 0; i < p; i++) {
			if (!is_ascii_alphanumeric_char(p_path[i])) {
				found = false;
				break;
			}
		}
	}
	if (found) {
		return p_path.simplify_path();
	}
	Ref<DirAccess> dir = DirAccess::create(DirAccess::ACCESS_FILESYSTEM);
	String path = p_path.replace("\\", "/").simplify_path();
	if (dir->change_dir(path) == OK) {
		String cwd = dir->get_current_dir();
		cwd = cwd.replace("\\", "/");