The reality is this. We want to know the temperature of the air entering the cylinders. Measuring the air temp in the Y pipe is pretty close.
Measuring the air at the filters works decently. The hot air entering the airfilter preheats the stock intercoolers, which then work to maintain that tempreature in typical driving. Racing is different, and dynoing really overheats the intercoolers. But for just driving around with the occaisional blast, measuring the air at the filter works pretty well. Some of the MAP ECU guys do it this way.
If the intercoolers do heat-saturate, and the air entering the engine is hotter than what we measure, the engine will run a little richer, which is not necessarily a bad thing........
Bob