Tony Athens, the author of that article, preaches several things over on boatdiesel: design your exhaust system so that water can't back up and ruin your turbo/engine, prop your boat to reach rated rpm at wot + 100, cruise your boat at several hundred (depends on engine) rpm below wot, feed your engine clean fuel with proper filtration. Probably half or more of his posts deal with one of these issues.
There are three cardinal rules discussed in that article on exhaust system design:
1. The spill over point at the injection elbow should be at least 12" above the water line.
2. The water injection should be down hill so an internal failure can't back flood.
3. An inherently safe exhaust system has the level of the spill over point aft of the water lift muffler below the spill over point at the injection elbow. That way repeated waves crashing on the transom can't build up a level in the water lift muffler to the point that it floods the engine.
On my Mainship Pilot 34, 1 and 2 were wrong with only 8" of clearance above the water line. I fixed it by raising the dry riser to allow 16" of clearance and pointed the injection elbow down.
David