The entire point of the system of record feature is that nobody is able to manually apply or remove the "sent" label.
Besides, since in the proposed solution the system is creating the filter, it could bypass checks that require the label not be sent. Just because it shows in filters, and it can be removed from filters by the user, doesn't mean it has to be able to be created through the normal filter mechanism. You still have a "system of record", if that's how we want to refer to this feature, it just requires a single initial setup step on the first received email that is intended to be kept as sent. That's entirely in line with how Gmail currently does things, such as allowing alternate From addresses (which requires an authorization step).