The IAT sensor visible via OBD is located in the manifold and is part of the Manifold Absolute Pressure sending unit. There is another IAT sensor at the air filter, but you can't read that one with OBD; you have to use DRB III.
The reason I believe this is the case is that when I disconnect the sensor sensor at the air filter, I get corresponding engine codes indicating MAP/IAT circuit high, but yet the IAT and MAP information reported by OBD is still active and produces good number. So this tells me that the MAP/IAT information reported by OBD is in fact inside the intake manifold, not at the intake filter.
Furthermore, what I have found is that the IAT sensor (reported by OBD) is very slow -- constantly integrating (averaging) temps as they vary. This cannot possibly reflect actual air temps, since air temperatures at the turbocharger compressor output can easily jump 200 degrees or more within a short couple of seconds (under acceleration). The intercooler probably cools by 100 degrees, but I would think (I have not measured it) the wide temperature excursion would still be reflected at the intake manifold (say, 300 degrees compressor output, cooled to 200 degress by the intercooler)
Watch IAT via OBD some time on a hot day in city traffic -- it will slowly climb at a stop light due to heat soak, and then slowly cool back down with vehicle movement.
OT: your data are interesting . Unfortunately, there could be many variables that could confound the results, such as temp probe speed, proximity to metal, etc. to interpret, we'll need to know some additional information:
1. metal AFE torque tube? home made home depot type?
2. is the temperature probe a metal tip or is it an exposed thermocouple bead type thermoouple? how big is it and how fast does it respond?
3. did you put a temp probe behind the radiator fan or near (but outside) the filter element?
measuring a higher temp inside the torque tube suggests some kind of heat soak. no, there is no hot air exiting the intake system as cool air enters -- molecules of air are flowing into the filter media and into the turbocharger, not out of it. They slow down inside the filter itself (large cross sectional area), and then accelerate again in the torque tube. if the torque tube is metal, it could transfer heat from the engine compartment to the air (or the temperature probe, depending on how it was installed).
the best way to measure these temps is to use a minimally protected type K bead type thermocouple located in the center of the torque tube cross section (avoiding torque tube wall proximity). such a probe looks like two wires twisted together with no visible "probe" on the end. These guys are VERY fast and will respond instantly. I used such a probe to further study the 03-04 turbocharger. results in TDR issue 48. The problem with general purpose metal probes is that they are just plain slow and don't give the real dynamic picture.
OT if your temp probes looked like two wires twisted together (with no "end" on them) then you probably got very accurate numbers. These can be slipped inside the AFE rubber coupler and into the torque tube and would probably be accurate, unless of course the tip itself is close to a torque tube wall. if your probes had a metal tip they are probably slow and subject to measurement error due to heat soak.
The other thing to consider is that the air flow under the hood is very complex. In order for cool air to come in via the SRT-10 hood opening and do any good, it has to have a place to go. otherwise, very litle air will actually enter that opening. My point is that the radiator fan may produce pressurized air over the engine which might tend to resist the flow of air trying to enter the engine compartment from the hood. thats what I suspect, anyway, as an explanation for your numbers.
If you have time, I'd suggest you go back to a dealer and inspect the SRT-10 truck itself (engine compartment), to see if you can tell what role the radiator fan might play there as well. maybe the whole hood thing is cosmetic on the SRT-10 as well.
it does surprise me that intake air temps measured close to the AFE filter would be hotter than under hood ambient. that result begs for more investigation.
Attention: TDR Forum Junkies 
For some time now I have been wondering the net affect of the SRT-10 hood and what, if anything, it brought to the party relative to air temps. Well my local diesel shop loaned me a Wavetek monitor which has two temp probes that we set up under the hood. The one monitor we hooked to the dip stick and overhung it by a couple inches. The other monitor we put inside the air intake system after the filter and just in front of the torq tube on the AFE air intake system. The ambient temp for the test was 54. 7*. My underhood probe averaged 22* to 24* at 75mph for 50 miles. The air intake temps averaged 62* to 64* and those temps were measured simultaneously while the underhood temps were taken. I did this test with the opening in the hood both blocked and open and all under the same test parameters. The net effect of cooling provided by the hood was negligible (+/- 5*). 
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