If the ship is at sea (>12 NM) it can be put directly into the ocean but when it comes close to land it needs to be mashed up and disinfected. Also there are some places called special sea areas that have different rules even if you are more than 12 NM. There are different rules for less then 3 NM and between 3NM and 12NM too.
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.