I think it would be easy to assume the bonus points are tied to the bonus level in Shooting Range, for several reasons. Honestly, the bottle stage is the easiest one and it's safe to assume that your accuracy is higher there than in other stages where the targets are actually moving. And in Shooting Range, I honestly don't think the Zapper feels as accurate as it does in first-party games. The hit boxes may just be a bit... off... compared to in Hogan's Alley or Wild Gunman.
Let's say the cutoff for earning the bonus is a hit rate of 90%. (I don't know if that's true, but it's a good guess.) I think a good run in the first two stages could still only put your accuracy at around 85%. Then, you suddenly ace the bottle stage, and your game-wide accuracy bounces up to 93%. Hello, 10k bonus! Then, as long as you can muster 85%ish again in space, you should stay at 90.1% or better for the game.