The design is to get the exhaust above the waterline then inject water so that it runs downward to the exhaust exit which looks to be below the boats waterline. Many ways are used to solve the exhaust problem. If it is working I would not mess with it.
Regarding the exhaust manifold flange, how many studs or bolts are on the exhaust manifold. My Perkins has 4. The engine builder made that decision. If only two I would expect the studs to be large. I would monitor the flange to assure no cracks in the metal.