In LTN you can limit stops to the number of vehicles in a train. All ships have a vehicle count of 2 and that means you can't limit a train stop to the small boat or the cargo ship. And you need quite different train stops for them.

So I wonder if maybe the vehicle count could be changed. The cargo ship could be split into nose, hold and engine so it has a count of 3. Or the personal boat could be split that way. I don't know if this can be done without moving the spots where inserters interact, so maybe that has to be an option.

Glad you're making use of the LTN Port capabilities. You can use LTN network IDs to segregate ships and boats. No reason to make unnecessary wagon entities.