There's a double-edged sword when it comes to "storing". The question remains: "to fill or not to fill".
The preferred method is to store empty. BUT, and here's the but.....can one really get all the fuel out? No, especially with built-in fuel tanks. You'd have to remove the sender and literally siphon every last drop out? Why so anal you ask? Because if ANY is left over, and with the now great area of "air" in the tank the gallon that remains will quickly phase separate {even treated}, and cause running issues down the road. Now the motor. You'd have to drain the fuel system including the VST, lines, injector rail, etc. Not easy. Bigger problem? Think of this analogy......throw a piece of raw metal into the ocean. It will actually survive LONGER than when you take it out and expose it to the air, where rusting ensues immediately.
The second method is to store it full. We store over 1000 boats here, and I ask all of my customers to have as fresh a fuel supply as possible, with it being topped off with 91+ octane. Treated properly, it has proven to be good fuel {at least here in the Northeast} as long as it is used with the advent of Spring time. Any longer than 7 or 8 months and it becomes a crap-shoot. As a percentage, I probably see a fuel-storage issue of about 1-2 percent. Full tanks are less apt to phase separate {due to the lack of available space in the tank}, are less explosive , and the motor internals are bathed with the treated fuels. Fuel pumps, injectors, any "metal" are immersed and protected. I discuss this very issue with Merc every year.
One of the most important components of winterization is to MAKE SURE you allow the treated fuel time to circulate throughout the motor. 5 minutes will not do it. The smaller the motor the longer it takes. I recommend to put the treatment in at your last outing {you should be using it ALL the time anyway}. We see an average of 15 minutes at idle.
EDIT: The sole reason for all this "stuff" is due to E-10 fuel. The older MTBE fuels were much less of a problem.