It sounds to me like Apple could break out Messages from SMS and then Messages would just be another competitor on the market like FB Messenger, whatever the fuck Google is running now, WhatsApp, Signal, etc.
FWIW Beeper's 'esoteric' fix is a gaping security hole. Their product relies on MITM and they're obviously not going to profit off of a minimal subscription fee if they're buying Apple hardware to make it happen.