You could use 2 way valves. I like the combination of the 2 way from manifold to desalination feed and the 3way at the LP pump because it gives backup protection for a hard to detect leak. In any case a valve between the salt water manifold lets you change filters or work on your desalination system shut off from sea water--also operating the diesel or generator if you do have a leak in your desalination loop. There is one more advantage--you can leave the hose between the manifold and the desalination in fresh water vs salt water.
But, yes, you can accomplish the same thing with 2 ways that are operated in combinations.
Let me add another thing to the post. In some Amels there may be another potential source for a fresh water leak into the manifold--a 3 way or double 2 way valve to the a anchor wash pump output that allowed fresh water chain washing. I think I remember some owners posting that they had this feature.
Bob, KAIMI SM429
Sipan Island, Croatia