Eveofchaos
The fact that it was introduced makes me think khan will take the offer but I really hope he doesn't. His goal is the Nek and returning to Liza. Being a pilot only progresses his rank in terms of information access. To resolve his issues with the Nak he needs to be strong, to survive on nitushe needs mana affinity. neither is granted to him with being a pilot.
Khan is very good at some things but he shouldn't aim to be good at all things. He has a knack for surrounding himself with people and should use it as he climbs to recruit talented individuals who will join him in his hunt for the Nak. I remember Eve mentioned an alternative title to the novel at some point which leads me to believe that, maybe, he will create a team of chaos users who have the same hatred as him.
Considering Khan's talent for fighting and engaging with aliens, adding on piloting shouldn't hurt him that badly. Plus it gives him an opportunity to make his own sort of new job position within the Global army. An ambassador who travels to meet new alien species and is capable of handling himself if those species are hostile, Khan suits that role perfectly. It means, he is not beholden to anybody when it comes to leaving a planet, as long as he is strong enough. Its literally everything Khan wants wrapped up in a bow. Maybe you add in Khan leading a team of people who are all similarly trained, but that would be at least a decade away, probably.