How would wiping off the bottom in the harbor avoid spreading the invasive species in that Harbor? The regs weren't being inforced by the locality to keep the local species in place in San Diego or Puget Sound?

If you want to keep species from being transported, it would make sense to make the boat's hull as toxic as tolerable to all species (which would include man)

There are a variety of reasons to require keeping bottoms clean, among them:

Save fuel usage;
Make the cleaning less disruptive of the bottom coating by making the cleaning less agressive;
use a paint that is effective but does not significantly harm other aquatic life -- as in creatures or growies.