### 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)

Variant ret = _GLOBAL_DEF(p_info.name, p_default, p_restart_if_changed, p_ignore_value_in_docs, p_basic, p_internal);
	ProjectSettings::get_singleton()->set_custom_property_info(p_info);
	return ret;
}
void ProjectSettings::_add_property_info_bind(const Dictionary &p_info) {
	ERR_FAIL_COND(!p_info.has("name"));
	ERR_FAIL_COND(!p_info.has("type"));
	PropertyInfo pinfo;
	pinfo.name = p_info["name"];
	ERR_FAIL_COND(!props.has(pinfo.name));
	pinfo.type = Variant::Type(p_info["type"].operator int());
	ERR_FAIL_INDEX(pinfo.type, Variant::VARIANT_MAX);
	if (p_info.has("hint")) {
		pinfo.hint = PropertyHint(p_info["hint"].operator int());
	}
	if (p_info.has("hint_string")) {
		pinfo.hint_string = p_info["hint_string"];
	}
	set_custom_property_info(pinfo);
}
void ProjectSettings::set_custom_property_info(const PropertyInfo &p_info) {