I look at it like playing a video game vs actually firing a weapon live.
Using Gunnery and AR, you're relying entirely on the HUD crosshairs and targeting data. Which would probably not be that dissimilar from playing an FPS game, since in those you often operate multiple weapon types with the same interface.
Firing live, you're actually having to line up the sights, etc. Every weapon behaves differently, so you need different skills for each category. Anyone who's fired a weapon in real life knows there's an entire body discipline that goes into shooting accurately.
Now, personally, I would have written the Drone modification so it's more expensive, and the weapon actually gets micro-servos installed so it can actually aim by itself, but the above is my justification for how the fluff might fit the rules as written.
-k