Jaguar has used a air/water IC built into the intake manifold, after the roots..

All of this is very hard to do without really compromising the length of the intake runners though... Ideally you should move the SC away from the engine the same amount that you're losing by putting an intercooler core inline. It's probably not that big of a deal starting with a type of SC that already doesn't have the greatest efficiency, but I still would hate to knowingly chip away engine efficiency.