The reality is a lot of boats are running around with misalignment. Especially the older Chinese built boats. Which can be hard to get into and/or keep in alignment without some re-engineering.
That is why I recommend using a coupling like these:
Marine Transmissions, Velvet Drive, Paragon, marine transmission parts, <marine transmissions>
Not a cure all by any means. But they will cut down on vibrations and protect your transmission.