Not sure about it 'not flushing the entire system'. Do we have facts that back that up? IMO, it would be unwise for Yamaha (or any OB mgfr) to recommend a system that would leave raw water un-flushed which would lead to premature deterioration of their product.
In talking to my Yamaha service folks (yes, I was unsure of the static flush at first), the entire system gets flushed on both sides of the impeller, which is why Yamaha tells you not to run the engine while performing the static flush or there may be damage to the system.
This makes sense to me, given that every orifice on the engine has water flowing through it during the static flush. Also, in my experience, the initial run of water is very warm when exiting the engine (and splashing all over me!), telling me that the water has run its course through the cooling channels of the engine.
I am satisfied that the static flush is very sufficient. But I'm not an 'expert'...