As ex-simple-aircrew, but with a legal education, I suggest that this is a bit like the difference between "not guilty" and "innocent". The law gives the benefit of the doubt to the accused (Chinook Mk2 safety). So it was "not guilty" because it could not be demonstrated that an airworthiness issue was the problem (so something/somebody else must be "guilty" - false logic but all too often used). As time progressed evidence assembles to the point that to a certain standard (the definition of which we can argue over) it is demonstrated that the accused is not at fault. Hence "innocent" or "airworthy" (equally invalid for reciprocal reasons).
Obviously, I do not believe this stands up. One of the big problems with safety critical software is precisely proving the negative - that there is nothing wrong with it. And aviation standards of engineering proof - 1 x 10-9 or whatever - are way beyond the legal standard of "reasonable doubt". But, critically in this case, they do not reach the required standard for the verdict of "no doubt whatsoever".
And so the Air Marshals' opinion fails.
Iain