### 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)

const String &prop_name = p_info.name;
	ERR_FAIL_COND(!props.has(prop_name));
	custom_prop_info[prop_name] = p_info;
}
const HashMap<StringName, PropertyInfo> &ProjectSettings::get_custom_property_info() const {
	return custom_prop_info;
}
bool ProjectSettings::is_using_datapack() const {
	return using_datapack;
}
bool ProjectSettings::is_project_loaded() const {
	return project_loaded;
}
bool ProjectSettings::_property_can_revert(const StringName &p_name) const {
	if (!props.has(p_name)) {
		return false;
	}
	return props[p_name].initial != props[p_name].variant;
}
bool ProjectSettings::_property_get_revert(const StringName &p_name, Variant &r_property) const {
	if (!props.has(p_name)) {
		return false;
	}
	
	r_property = props[p_name].initial.duplicate();
	return true;
}
void ProjectSettings::set_setting(const String &p_setting, const Variant &p_value) {