One of the many joys that Venice provides is the surprise at seeing things in unexpected contexts. Apply a little logic and you’ll rapidly realise that what you’re witnessing is probably unavoidable, but why spoil the magic of that surprise.
So a vaporetto stop has to be manufactured somewhere, and most likely outside of the city. Having made it, how else are you going to get it into place other than to drag it across the lagoon and up the Canalazzo to it’s resting place (in this case at the museum stop of Ca Rezzonico)?
Personally I prefer the fantasy of a water bus stop in the middle of nowhere; a place for a Venetian JK Rowling to site their equivalent of Platform Nine and Three Quarters maybe?