The amount of water it takes to get into the air intake of the engines, is certainly 100's of gallons of water. If you have all the compartment plugs in, as you should, the lower bilge does not hold much water. And the back of the boat, under the clean out tray, where the water boxes are, and the engine compartment, is pretty much the only place water can gather...until it is flowing past the engine compartment bulkheads into the seat compartment either side of the boat. While this can happen fast, it isn't unnoticeable. And all that weight in the very stern will bog down the boat.
I am willing to bet that yamaha had tested this very scenario multiple times. Since the 90's, yamaha has built these boats with clean out plugs in virtually the same design as they do now. And I am sure they have been challenged a few times. And they continued to build the same basic design. The made the lower shell of the plug (ABS) narrower, so that it wouldn't be so critical to install/remove, they offered rebuild kits. But overall, the plug design and use is the same. this scenario isn't as incidious as it has been suggested. And while I feel bad for the loss experienced by the OP, he is not a victim, and that is how this thread was presented. And in addition, it Implies that these boats are designed poorly, unsafe, and that Yamaha is the bad guy. These boats have known shortcomings but they are among the safest, and they are the best selling boats on the planet in their category. Regardless, it is imperitive that we understand these boats and their capability, as well as their shortcomings.