Tim, the other reason that you should grease the front axle is because there is room for you to install and remove the axle bolt without having to heat or cool various parts. From a maintenance perspective that's a good thing, however the dilemma with that is two fold: 1) enough room to easily put the bolt in means enough room for the bearings to spin on the axle, and not the races. Normally that's not the case, but when the suspension is ratcheting up and down, it happens often enough to be a concern. 2) If there's room around the bolt, that means there's not a seal there. Any water you come across (not even ride through, just riding in the rain or splashing along in puddles) will be drawn to the inside 'safe space' between the bearings. The axle bolt is designed to keep the front tire on the bike, not guard against corrosion. As a result, any water you get in there will do what water does and start breaking everything down to it's base elements. As for the airbox, there are very rapid pressure changes that occur inside when the bike is running. Think of it this way: The fuel/air mix from the carb wouldn't go anywhere if there wasn't a vacuum to draw it into the cylinder. That's why timing and valve adjustment are so important on an engine. When the air starts moving from the airbox into the carb, that would naturally create a low pressure zone in the airbox. Air is drawn in from outside to airbox to try and restore a pressure balance. If the engine can't breathe freely, you would be slowing that movement down, and thus reduce engine power. You had mentioned the carb throat being smaller per square in than the airbox openings. That smaller size is required to create the venturi that will draw the fuel up out of the float bowl (through the jets) and create the fuel air mix. So the short answer at the end of this very long response is this: It's not the size that matters, it's how you use it!
Hope this helps shed some light on the questions you presented.