That water is much hotter than ambient air, but it is far more thermally conductive, absorbing a lot more heat than the same volume of air. I think the "air to air intercoolers are more efficient than water to air ones" has more to do with the relative size of each one. The water intercoolers I've seen tend to be tiny, compared to huge air to air ones. I bet a similarly sized water intercooler could outperform an air-air one.
I know air to air is more effecient. Thats why semis, light duty, etc run them. I was just curious why large equipment would run both. Your engine water temp should be below 200. The air coming out of the air intercooler is hotter than that so by Fourier's Law (law of heat transfer/radiation) which states heat flows into cooler bodies, it will not heat up, the water will take out heat. The amount the water takes out will be not as large though.