### 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)

PackedStringArray unsupported_features;
	PackedStringArray supported_features = singleton->_get_supported_features();
	for (int i = 0; i < p_project_features.size(); i++) {
		if (!supported_features.has(p_project_features[i])) {
			
			if (p_project_features[i].begins_with("Vulkan")) {
				continue;
			}
			unsupported_features.append(p_project_features[i]);
		}
	}
	unsupported_features.sort();
	return unsupported_features;
}
const PackedStringArray ProjectSettings::_trim_to_supported_features(const PackedStringArray &p_project_features) {