I just started reading the Alpha Strike book and I am wondering the same thing. In addition to Weapon Specialist, the multiple attack rolls method doesn't seem to work with the Float Like a Butterfly or Lucky SPA. Also, the Marksman and Sharpshooter seem kind of gamey with this.
I know you're supposed to work things out with your opponent, and that's fine, but I would really like to know how these were intended to be played.