The link for the 2nd photo is taken from where the front passenger wheel was ( on a right hand drive car) looking forward. The new intake is at the top of the photo with the opening pointing towards the side of the car with the inlet vent about 4 inches below it (on the outside this is the small vent next to the fog light).
The original intake was about the same height, but with the resonator box in front of the vent I imagine that going through a deep puddle would force water up towards the intake, where with the new intake, any water coming in through the front vent can go straight past the vent and out through gaps in the undertray.
I had thought that it would be nice to take advantage of the ram-air effect of connecting the intake directly to that vent, but as you said could cause problems in wet weather.
While I was fitting all this I did notice a couple of small holes in the bottom of the airbox which I assume are for letting water out of.
Now that I know where the intake is I will definitely be more aware of deep looking puddles.