Yeah, NPC pilots keep the same royalty rate that you hired them on, even after they level up.
The NPC is not actually in the fighter (SLF), but controlling it by "telepresence" (ie remote control). Same if you fly the fighter. If the fighter is destroyed the pilot/you are still safe in the ship and just need to wait for a replacement fighter to be synthesised in your hanger before pilot/you take off again in the SLF. Higher class fighter hangers have more synthesis iterations.
If your ship (ie mothership) is destroyed, you automatically jump in an escape pod, are mysteriously rescued and ready to rebuy your exact same ship, engineering and all (you lose cargo, exploration data).
However, your poor hapless NPC crew member is not so lucky. They have no escape pod and are consigned to the cold black void. Now you have to hire & train a new one.
Twisted mechanics right?
If you intend on getting blown up a lot, just hire an expert NPC rather than investing the time in training one. Chances are they will die just as they become useful (ie expert).