But isn't the 'net positive', itself only a factor in the very last stage of all of the input energy required for ignition? So they need to factor in all other components before looking at these orders of magnitude being useful?
No, it's not. If you get to arbitrarily define at what point you count "energy in" (as the NIF people are), you could also define a clever spot for MCF to be net positive.
NIF's definition of Q was defined by the National Academy of Sciences and is analogous to the Q that MCF uses.