The reason for the multiple spark is to help burn any residual fuel left from the first combustion. It's not much but like everyone says...every little bit counts. A stock engine works fine with the stock spark. When you raise compression ratio and start adding more air and more fuel necessary for the bigger bore engines, then the stock spark just can't burn all of that fuel in time. If you drop a match in a full bucket of gasoline the odds of it lighting the gas is pretty low. If you drop 2-3 matches immediately behind the first match, your chances of ignition are higher because the flame front is stronger and longer.
I'm an MSD guy myself becuase I was using it before the Flame ever came out. I'm sure the Flame TL is awesome but it's still very expensive. Of course in order to use the full capabilities of your new expensive toy, you need the software and computer lead to program it. Plus if you currently use an MSD TL setup, you have to buy a used e-box with most of the guts just to be able to use it. Since it's going in the stock e-box, you're also limited on what coils and starter solenoids you can use. In a bind, I like knowing I can run to the local motorcycle shop for another coil or to any auto parts or hardware store for another starter solenoid. I do worry about taking my MSD in the salt water but it's rare that I go in salt water so it's less of a big deal. If I ran salt more often, I would put it in a waterproof box or I'd have something else.