If all that can be flushed is human waste and paper, then why not put it directly into the ocean? It's quickly and completely bio degradable (eaten by fish and micro organisms).
Having one system for when the ship is out at sea and switching to something else causes even more engineering problems. Even if you're not processing the waste, the vacuum sewage system would still be used to collect the waste to discharge it.
MARPOL Laws: http://www.imo.org/en/about/conventions/listofconventions/pa...
https://www.dco.uscg.mil/Our-Organization/Assistant-Commanda...
Special Sea Areas: http://www.imo.org/en/OurWork/Environment/SpecialAreasUnderM...