"In general, the skill ranks of an NPC crew member are equal to the CR of the NPC or the tier of the enemy starship. To determine the skill modifiers of an NPC crew member, first decide whether the NPC has mastered the skill or is simply good at the skill. Usually, one crew member will be a master at one skill; the res tof the crew will have good skills. The skill modifier for a master skill is equal to 9+1.5*the NPC's ranks in the skill. The skill modifier for a good skill is equal to 4+1.5*the NPC's ranks in the skill."
NPCs use their own rules, which is the part you're missing. I haven't followed SF from before its release so I can't speak directly to any designer intent that was stated back then, but I've seen mention of a general trend of NPCs having high attack and low AC compared to higher PC AC and lower attack, and the total gunnery modifier there follows that trend. Nevermind that gunnery isn't actually a Piloting skill check - presumably NPC attack bonuses follow much the same formula, since it lines up exactly with the final values the Tyrant has.
As a side note, a character starting with 18 in Dex can hit +24 by 16, not just +21. 18 (+4), +3 from level for 21 (+5), +6 from personal upgrade for 27 (+8), +16 ranks or BAB. This is also the same value the Tyrant's gunners have before the +9 for apparently being masters of shooting things in space.