When a gun can hold less ammo, the shooter is forced to reload more often, thus giving more people time to escape. And if you think those few seconds don't matter, look at the Dayton shooting. Police stopped the shooter in thirty seconds, which is very commendable, but in those thirty seconds, he killed fourteen people. A few seconds to stop and reload really do matter.
You're right, the number is pretty arbitrary, but I'd rather have a low but arbitrary limit than no limit. Should a gun be able to hold six bullets or ten bullets? I don't know, but either number is better than fifty bullets.
Which is why I think we shouldn't stop at rifles. Much of the focus, when it comes to gun control, is on guns when we should also be talking more about gun accessories and the screening process.