In the Japanese version, if Zonk fuses with Moo Moo, he will transform into a female lady and will have the ability to shoot milk bombs, which are supposed to resemble a woman's breasts and the milk coming out represents breast milk. The American version changes this by replacing the breasts with ordinary milk bottles and changing Zonk's entire body to not look like a lady.

In the Japanese version, if Zonk charges his ability to the max, he will drop a piece of poop. This was changed to a bomb/rocket in the American version. This change also applies to other poop-like sprites seen throughout the game as well.

During development of the English translation, Air Zonk had a couple of name changes. The first name was going to be "Bonk's Thunder Shooting", which at the time, Zonk still had the same name as Bonk. The second name change was then going to be "Bonkinator: Cyborg Punk", which was going to be a very similar title to the Japanese title, PC Denjin: Punkic Cyborgs. It was then decided to change the name to "Air Zonk" in the final release.

The game's intro differs between versions. In the Japanese version, Zonk will be seen ramming through the logo, while the American version will show Bonk on top of a building turning into Zonk and then flying off screen. The game's American intro can still be seen in the Japanese version if the player doesn't press anything on the title screen. The game's demo at the beginning of the game was also changed due to the intro change.