In this case, the fish isn't a closed system. It's harvesting energy from the moving water, which requires external energy from the sun to keep the water cycle going.
His claim about a sailboat not being able to exceed windspeed sailing directly downwind is deceiving because it is definitely not the fastest point of sail. I believe this is done for dramatic effect to make Blackbird's feat sound more incredible. Sailing close hauled, almost directly into the wind, can achieve double wind speeds near effortlessly on low draft racing multihulls, and possibly on land with whatever those sailing carts are called. Of course, directly downwind is the only course for this experimental propellor craft, thus the only criteria.
But that's the entire point of Blackbird: to show that it is possible to sail directly downwind faster than the wind. It is not immediately obvious that this is possible.
(JK, don't cite me in physics class!)