I know this has been a hot topic lately, because of the E-10 gas, (top-off, or empty?). Imo, it's a tough call. I completely agree with those that say, less fuel, less expense, (if there's a problem after storage). At the same time, less fuel in the tank means more air space, and possibly more water contamination due to condensation. Some manufacturers are still recomending "top-off", (full). According to what I've read, it's not just a case of less fuel, more air space, but more because the ethanol in the fuel "attracts" water, and that compounds the "air space" problem.
I honestly don't know which is the "absolute best" way, but for now I'm still going with 3/4 full, (or better) and treated. That's for 5 to 6 months of storage. If I were storing a boat for a year or more, I would go with completely empty.
I also think it's very important to run your motor, (under way) long enough to make sure the newly treated fuel gets through the engine.