I can see what you are saying with transients. But by definition boats that are sitting in a marina getting regular (monthly or whatever) hull cleanings are not the ones coming from or going to different watersheds/areas. In order for that to work the rule would have to have you sitting at the Police Dock waiting for new arrivals and springing into action to clean their bottoms that one time/place specifically.
Likewise with boats leaving -- which is a tiny percentage of marina slipholders. I know because as a transient good luck getting a slip there - they are all taken by locals (not that there is anything wrong with that; I'm just saying that the vast majority of slipholders in SD who are going to be affected by this are locals who do NOT go to different aquatic areas.
So that doesn't make sense to me.
(I do see what you are saying, but just not in this application. For example in a state with a lot of trailerable skiff-type fishing boats, people are supposed to clean and bail them before launching on a different lake. That is where you can easily have lots of people moving "foreign" species around.)