It's not a matter of either one getting more air.... Actually the stock air box flows as much as any 3" piping and big cone filter will and it gets its air from forward of the firewall. The issue with the stock air box is just idiots using cheap ass filters which flow less than a coffee filter. The stock filter has a LOT of surface area and actually requires the air to change direction less than a cone filter.
The pipe to run under the headlight is L shaped with about 12" on one end and 6" on the other. Put some thick rubber along the edge of the firewall's oval opening so it doesn't cut into the pipe.
Rain won't affect it at all... less so if you have your fog lights in place (echo... echo...). As for driving through flooded areas deeper than the height of your fog lights... well, you've got bigger problems. As I said, there are ways to ensure that you don't suck up a bunch of water should you try to go canoeing anyway. They should be covered in the FAQ thread. One is a small conical filter which sits between two pipes like a coupler. It's restrictive enough that it doesn't pull in air unless the filter is blocked. The other is a spring loaded relief valve. At any rate the filter should sit behind the bumper between the fog light and head light so it'll see almost no moisture. Be sure to install this while the head light is DOWN!
The upside to moving the filter forward of the firewall is that you don't have work to ensure the box seals off from the engine bay when the hood is closed or has its own lid to bolt on. Another downside to a box is there's a greater volume of air to heat soak at idle and low speeds (same goes for running larger IC piping than you need
). In all cases it's a good idea to get all intake and exhaust piping ceramic coated.