Take a look at the solution provided in this thread: https://forum.arongranberg.com/t/how-to-deal-with-the-new-tiles-type-unsafe-span-removing-nodes-marked-as-unwalkable/15716
We used that solution as our basis, combined with seed points. So the pruning uses a bunch of points, at least one of those points needs to be reachable, otherwise the polygon is pruned. This makes all those tiny isolated islands go away.