As for what some others are doing, my flying buddy just did a Seamaster with the ESC behind the motor and the batteries under the wing. Flys great! No issues with bench testing and three flights from water so far. He used a Turnigy motor and ESC.
I am doing mine now with the ESC in the forward area under the wing and the batteries accessed thru a hatch in front so the wing doesn't have to come off for battery changes. Seems to balance just fine. I am using a Rimfire motor and CC Phoenix 60 ESC with a TP 5S2P 4400mah Lipo.
As for cooling the ESC, I always oversize the ESC and enclose them in the hull. I depend on the volume of air in the hull and the fact I never stress my components to their limits. Been flying a Drake II seaplane for three years now with no issues. Also an Aventura Twin and a Aquastar. Built two more depron Drakes this year and did the same with no issues.
As for why it might damage components, it seems like after ESC pulses the motor, little current is needed from the battery and the field collapses around the wire generating "ringing" (a spike in voltage) on the battery wire which can destroy the ESC if large enough. This is not uncommon in electronics and you would be able to see it if you had an oscilloscope. I would think the issue would be more common with large cell counts. These are my words, not from the article, and I take no responsibility for them!!