The difference is that NAUI, SEI, CMAS, and a few others believe that watermanship skills are important to anyone who will be around said environment. Underwater swims are part of that. These are the foundations of the programs. They then progress to snorkeling and skin diving skills before a student even gets on scuba. Before they even get a breath off of the reg they have learned to successfully clear a fully flooded mask underwater, simulated clearing a reg (using the snorkel), learned how lung volume affects buoyancy control, and how to move efficiently underwater. I see absolutely nothing silly about that.
Before a student even gets on scuba they will take and place their mask and snorkel on the bottom of the pool, surface, move away from it, then swim 25 feet underwater to retrieve said mask and snorkel and before surfacing have the mask clear and snorkel breathable when their head hits the surface. A great confidence building exercise as well and clearly demonstrating the benefits of proper breathing, buoyancy, and clean, efficient movements. What is silly about that? Because to successfully perform this they need to have the basics of moving underwater down. The swimming, treading, and underwater swims see that they do. I still don't see any silliness.
If anything is silly it's putting people who can't swim without fins, mask, and snorkel in the water at all. Let alone on scuba.