[don_mondo]

In the 7th edition rule book it states that you need to have a full organization chart of 1 HQ and 2 Troops alongside all the other conditions to gain the bonus.

Which bonus are you referring to? Objective Secured? If so, then the answer is that GK using the Nemesis Strike Force do not gain Objective Secured. They have their own 'bonuses' (Command Benefits) listed in the codex that the GK NSF gains (Brotherhood Commander, Rites of Teleportation).