NPC's are characters who, while getting some characterization, are not the main priority in the story. For example Paul Lyons in Gundam Crossover - Those Who Correct finds a Lancer companion in Graham Aker whom is an NPC. He will be the main contrast to the more stone cold militaristic soldier that Paul is and help him develop out of it. However Graham himself could indeed die without Paul, a main character, being much affected by it in terms of being able to continue the roleplay. Unless the NPC is essential, like Captain Jason in the roleplay, then the case is that he is simply a figure head who is there to be the figure head and mentor without the need to make an entire character like I did Paul. 

In other words NPC's are there to advance the roleplay while the main characters are there to be essential to the roleplay's continuation. They are the main focus and are the main reason for what is going to happen and will happen in the roleplay. An example of this is it Graham had a 'heel' turn and became Paul's enemy it would mean Paul would need to overcome a close friend in order to move on. If Jason died Paul would need to step up to lead the crew in his stead. It's all about advancing the player character.