### 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 (PackedData::get_singleton()->is_disabled()) {
		return false;
	}
	bool ok = PackedData::get_singleton()->add_pack(p_pack, p_replace_files, p_offset) == OK;
	if (!ok) {
		return false;
	}
	
	DirAccess::make_default<DirAccessPack>(DirAccess::ACCESS_RESOURCES);
	using_datapack = true;
	return true;
}
void ProjectSettings::_convert_to_last_version(int p_from_version) {
	if (p_from_version <= 3) {
		
		for (KeyValue<StringName, ProjectSettings::VariantContainer> &E : props) {
			Variant value = E.value.variant;
			if (String(E.key).begins_with("input/") && value.get_type() == Variant::ARRAY) {
				Array array = value;
				Dictionary action;
				action["deadzone"] = Variant(0.5f);
				action["events"] = array;
				E.value.variant = action;