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The beauty of owning a Mustang is the ability to mod it till the cows come home (I'm in the midwest don't you know). If a stock 5.0 is able to handle boost, I would think the heavy duty Boss engine would be especially able to take it. As far as the tranny, I guess we'll have to wait and see.
I'm also a purist - one of the things that sold me on the Boss is that it was naturally aspirated. But, that's just me and some of you like minded folk. There's room in the stable for boosters as well - no limits. If you have the money and inclination, make it fly!