### 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)

vc.flags = PROPERTY_USAGE_EDITOR | PROPERTY_USAGE_STORAGE;
		}
		if (v->internal) {
			vc.flags |= PROPERTY_USAGE_INTERNAL;
		}
		if (v->basic) {
			vc.flags |= PROPERTY_USAGE_EDITOR_BASIC_SETTING;
		}
		if (v->restart_if_changed) {
			vc.flags |= PROPERTY_USAGE_RESTART_IF_CHANGED;
		}
		vclist.insert(vc);
	}
	for (const _VCSort &E : vclist) {
		String prop_info_name = E.name;
		int dot = prop_info_name.find(".");
		if (dot != -1 && !custom_prop_info.has(prop_info_name)) {
			prop_info_name = prop_info_name.substr(0, dot);
		}
		if (custom_prop_info.has(prop_info_name)) {
			PropertyInfo pi = custom_prop_info[prop_info_name];
			pi.name = E.name;
			pi.usage = E.flags;
			p_list->push_back(pi);
		} else {
			p_list->push_back(PropertyInfo(E.type, E.name, PROPERTY_HINT_NONE, "", E.flags));
		}
	}
}
bool ProjectSettings::_load_resource_pack(const String &p_pack, bool p_replace_files, int p_offset) {