Man, am I glad I was occupied with other stuff! I am guessing you guys are pretty convinced up front, even though you say your open to what may be the reasons.
@upperdeck is right on the money...and, if you prevent water in a compromised hull from invading all the space in the boat, it has to fill the void of the bilge first before it goes elsewhere, and the only way for it to go elsewhere is through a small opening in the back of the engine compartment that connects that lower bilge to the engine compartment, where the bilge pump sits. It is a small semi circular opening and sure, it will back fill fast. Your upgraded pump
@Addicted, will only pump what it will pump, 500/1000/1500gph or whatever it is.
There is an exception to every rule I am sure, maybe more than one. But going with the odds, you would be better off plugs in on the water, and out when water is present in the compartments or may be present. That means that if you store the boat outside where the cover may be compromised, you should leave all the plugs out.
Now, on my 230, the ski locker did not drain into the fuel compartment, it drained into that area below the ski compartment and ran under the fuel compartment back to the back bilge area. We are talking about an area no more than 1" high. It is just the space between the floor level hull section and the outer hull. It isn't designed to hold water, just drain it. If a breach allows water to force itself into that entire area with plugs open, it fills the open compartments. And another reason you don't want water forward in this boat...the water filling the forward end will lift the stern out of the water, possibly removing the bilge pump from the equation.
Yamaha doesn't say leave all compartments open when out of the water, they say they should be open if water is present. I add that if water "may" be present, they should be left open. None of this is an argument. Any of us can come up with a scenario that it may be better in or out in that scenario. But I have had interaction with most all of you and know some of you personally. I can say that while it may be that one of us may scratch our heads in disbelief, that disbelief is probably that we can't seem to communicate with the other what we mean, not that the other is stupid. I have been accused a number of times of arrogance just because of my writings. And I am not any different than anyone else, and can become defensive.
I just don't think you can account for all situations, and rational of one mind versus the rational of and entire engineering, R&D, legal, marketing, etc., departments, and as one mind, I always know I may misinterpret. And that is when I look to what the consensus is. As some others mentioned, it is your boat, you are the captain, if you feel you can explain your position in a court of law if it ever came to that, then by all means, no worries. But my fear is that I overlook something when if I operating outside of SOP (standard operating procedure)...and that is going to be critiqued by the masses. So if you run outside of SOP, then you will lose the argument whether or not your opinion was right or wrong, because you become a test pilot when you disregard SOP and go off on your own. Just the way it is. Anyway, I see this thread as educational for all of us. And maybe through continued comments, something becomes more clear for me, who knows!