### 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 features;
	features.append(VERSION_BRANCH);
#ifdef REAL_T_IS_DOUBLE
	features.append("Double Precision");
#endif
	return features;
}
const PackedStringArray ProjectSettings::_get_supported_features() {
	PackedStringArray features = get_required_features();
#ifdef MODULE_MONO_ENABLED
	features.append("C#");
#endif
	
	
	features.append(VERSION_BRANCH "." _MKSTR(VERSION_PATCH));
	features.append(VERSION_FULL_CONFIG);
	features.append(VERSION_FULL_BUILD);
#ifdef VULKAN_ENABLED
	features.append("Forward Plus");
	features.append("Mobile");
#endif
#ifdef GLES3_ENABLED
	features.append("GL Compatibility");
#endif
	return features;
}
const PackedStringArray ProjectSettings::get_unsupported_features(const PackedStringArray &p_project_features) {