The simple answer: You've got two heat exchangers. There's a loss with each one.
Long answer:
For the sake of arguement, lets say that all heat exchangers are 90% efficient, and our scenario is ambient is 305K and the pre-IC compressed air is 340K. Other than doing my PV=nRT calculations, I have no idea what the pre-IC temps are at high boost levels. 340K is roughly 150F... For all i know its much hotter, so keep in mind my overall numbers may be pretty off.
For an Air-Air IC:
You get 90% of the 35K difference or remove 31.5K off the intake charge and come down to 308.5K.
For an Air-Water IC:
You get 90% efficiency for EACH exhcange (intake charge to water, then water to air). So you only get down to 311.65K, with the water being right in the middle at 308.3
But that's steady-state. Most of the time you're not running full boost, so your intake charge is only, say 310 around town. In that case, the water is around ambient of 305.5. So when you punch it, you've got virtually the same performance as an air-air.
It's also over-simplified. Touch your radiator after a highway drive, and it's cool to the touch. Now imagine it after a hot lap, you'll burn yourself. Around town, water in an AWIC is steady-state for town driving 305.5, and once you punch it, it'll slowly start to rise to the steady-state, but in the mean time it'll be relatively cool. Think of how long it takes to boil a gallon of water. For an auto-x you can take advantage of this by having an additional reservoir in the loop that's full of ice water. Think of how long it takes to boil 10 gallons of COLD water. By the end of your lap the water is warmer, but still colder than ambient and you're getting a benefit vs your 90 degree summer air.
If you alter the efficiencies, to say 95% for air-water and 80% for the air-air the numbers change again. Or say that a IC is more efficient than a smaller, and that your FMIC is larger than the TMIC. But the point is that you lose something at each transfer: nothing is 100% efficient.
I think that was a really rambling way of explaining if. Did it make sense?