Wouldn’t the trailered boat issue be solved most easily by requiring that the bottoms of the trailered boats and their trailers be hosed down with fresh water before backing the trailer into the water and launching the boat?
Currently the recommendation is to wash down the boat, trailer, engine cooling system and any systems that use raw water (Livewells, etc)be thoroughly flushed before the boat is launched into a different body of water.
The best idea I have seen for this is a fresh water hose available at the launch ramp area. This way the boat operator can hose everything down immediatly after pulling the boat out of the water.
At any rate EPA discharge permits won’t do anything to prevent the spread of species like the Milfoil.