Well, the cool thing about the Battlebabe is you can upgrade your guns from there...
1) Why is the rifle inferior to the shotgun? It does 1 less harm and is loud instead of messy (a limitation).
Because (3-harm far) is too badass for words, and loud means you either have to silence that rifle (a fair proposition) and it isn't messy like a shotgun. I could go into the pseudo-physics but basically ask yourself: "Which gun would I rather be shot with?" One that makes a lot of shreddy wounds, or one high-impact wound?
2) Why is "semiautomatic" the only way to get rid of Reload? Did bolt-actions meet the same end of second names in the Apocalypse World?
Think of the modifiers less as attributes of real weaponry and more like traits about your weapon that can be used against you by the MC if they so choose. Remember that it's 50 years after the apocalypse, so guns are unreliable by default, and you have to work your way into reliability.
3) Why is the rifle's range "far" and not "close/far"? Is there any reason for which a rifle shouldn't be effective when you can see someone's eyes? And why is "3-round burst" the only way to add "close"?
I kinda agree with you there. But it depends on the kind of fictional rifle you're talking about. Usually people take SWAT-style sniper rifles and are looking at weapons that do major harm at long distances with some set-up action. I mean, if someone's at close range with you, you've got about 5 seconds to take one good-placed shot before they really are
too close to use your rifle. Unless as a club.